5GPN | pdb_00005gpn

Architecture of mammalian respirasome

PDB DOI: https://doi.org/10.2210/pdb5GPN/pdb
EM Map EMD-9534: EMDB EMDataResource

Classification: ELECTRON TRANSPORT, OXIDOREDUCTASE
Organism(s): Bos taurus, Sus scrofa
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2016-08-03 Released: 2017-04-05
Deposition Author(s): Gu, J., Wu, M., Guo, R., Yang, M.
Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The architecture of the mammalian respirasome.

Gu, J., Wu, M., Guo, R., Yan, K., Lei, J., Gao, N., Yang, M.

(2016) Nature 537: 639-643

PubMed: 27654917 Search on PubMed
DOI: https://doi.org/10.1038/nature19359
Primary Citation of Related Structures:
5GPN

PubMed Abstract:
The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.

Organizational Affiliation

Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 1,741.77 kDa
Atom Count: 75,545
Modelled Residue Count: 12,814
Deposited Residue Count: 15,605
Unique protein chains: 63

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A, M	446	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P31800 (Bos taurus) Explore P31800 Go to UniProtKB: P31800
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UniProt Group	P31800
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B, N	439	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P23004 (Bos taurus) Explore P23004 Go to UniProtKB: P23004
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UniProt Group	P23004
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C, O	379	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00157 (Bos taurus) Explore P00157 Go to UniProtKB: P00157
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UniProt Group	P00157
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D, P	241	Bos taurus	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00125 (Bos taurus) Explore P00125 Go to UniProtKB: P00125
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UniProt Group	P00125
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E, Q	274	Bos taurus	Mutation(s): 0 EC: 1.10.2.2
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F, R	110	Bos taurus	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G, S	81	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13271 (Bos taurus) Explore P13271 Go to UniProtKB: P13271
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UniProt Group	P13271
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H, T	78	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00126 (Bos taurus) Explore P00126 Go to UniProtKB: P00126
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UniProt Group	P00126
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I, U	78	Bos taurus	Mutation(s): 0 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272 Go to UniProtKB: P13272
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UniProt Group	P13272
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J, L	62	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00130 (Bos taurus) Explore P00130 Go to UniProtKB: P00130
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UniProt Group	P00130
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	K, V	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07552 (Bos taurus) Explore P07552 Go to UniProtKB: P07552
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UniProt Group	P07552
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3	W	264	Sus scrofa	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase 75 kDa subunit	X [auth Y]	727	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa) Explore A0A4X1V1H9 Go to UniProtKB: A0A4X1V1H9
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UniProt Group	A0A4X1V1H9
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2	Y [auth Z]	463	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1S1A8 (Sus scrofa) Explore F1S1A8 Go to UniProtKB: F1S1A8
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UniProt Group	F1S1A8
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7	Z [auth a]	216	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa) Explore A0A8D1TL60 Go to UniProtKB: A0A8D1TL60
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UniProt Group	A0A8D1TL60
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8	AA [auth b]	212	Sus scrofa	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	BA [auth c]	464	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa) Explore A0A4X1SZP7 Go to UniProtKB: A0A4X1SZP7
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UniProt Group	A0A4X1SZP7
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	CA [auth d]	249	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SM98 (Sus scrofa) Explore F1SM98 Go to UniProtKB: F1SM98
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UniProt Group	F1SM98
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	DA [auth e]	318	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O79874 (Sus scrofa) Explore O79874 Go to UniProtKB: O79874
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UniProt Group	O79874
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	EA [auth f]	347	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O79875 (Sus scrofa) Explore O79875 Go to UniProtKB: O79875
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UniProt Group	O79875
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	FA [auth g]	115	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O79880 (Sus scrofa) Explore O79880 Go to UniProtKB: O79880
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UniProt Group	O79880
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	GA [auth h]	459	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O79881 (Sus scrofa) Explore O79881 Go to UniProtKB: O79881
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UniProt Group	O79881
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	HA [auth i]	98	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P56632 (Sus scrofa) Explore P56632 Go to UniProtKB: P56632
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UniProt Group	P56632
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	IA [auth j]	606	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q9TDR1 (Sus scrofa) Explore Q9TDR1 Go to UniProtKB: Q9TDR1
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UniProt Group	Q9TDR1
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	JA [auth k], KA [auth l]	175	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for O79882 (Sus scrofa) Explore O79882 Go to UniProtKB: O79882
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UniProt Group	O79882
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	LA [auth m]	84	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1VPG4 (Sus scrofa) Explore A0A4X1VPG4 Go to UniProtKB: A0A4X1VPG4
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UniProt Group	A0A4X1VPG4
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	MA [auth n]	99	Sus scrofa	Mutation(s): 0 EC: 1.6.5.3
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	NA [auth o]	106	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SV23 (Sus scrofa) Explore F1SV23 Go to UniProtKB: F1SV23
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UniProt Group	F1SV23
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9	OA [auth p]	377	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SL07 (Sus scrofa) Explore F1SL07 Go to UniProtKB: F1SL07
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UniProt Group	F1SL07
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	PA [auth q], TA [auth v]	357	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SIS9 (Sus scrofa) Explore F1SIS9 Go to UniProtKB: F1SIS9
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UniProt Group	F1SIS9
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	QA [auth r]	144	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A8D1NRT6 (Sus scrofa) Explore A0A8D1NRT6 Go to UniProtKB: A0A8D1NRT6
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UniProt Group	A0A8D1NRT6
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	JB [auth Aa], RA [auth t]	156	Sus scrofa	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5	RB [auth Ai], SA [auth u]	189	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SGC6 (Sus scrofa) Explore F1SGC6 Go to UniProtKB: F1SGC6
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UniProt Group	F1SGC6
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial NADH dehydrogenase Fe-S protein 4	UA [auth w]	175	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G8IFA6 (Sus scrofa) Explore G8IFA6 Go to UniProtKB: G8IFA6
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UniProt Group	G8IFA6
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	VA [auth x]	123	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1S031 (Sus scrofa) Explore F1S031 Go to UniProtKB: F1S031
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UniProt Group	F1S031
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	WA [auth 0]	261	Bos taurus	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	XA [auth 1]	147	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
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UniProt Group	P00423
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	YA [auth 2]	109	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
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UniProt Group	P00426
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	ZA [auth 3]	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
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UniProt Group	P00428
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	AB [auth 4]	84	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
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UniProt Group	P07471
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	BB [auth 5]	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
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UniProt Group	P00429
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	CB [auth 6]	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
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UniProt Group	P04038
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	DB [auth 7]	59	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
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UniProt Group	P07470
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	EB [auth 8]	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
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UniProt Group	P13183
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	FB [auth 9]	47	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
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UniProt Group	P00430
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	GB [auth s]	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
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UniProt Group	P10175
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	HB [auth y]	514	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
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UniProt Group	P00396
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	IB [auth z]	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
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UniProt Group	P68530
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	KB [auth Ab], QB [auth Ah]	134	Sus scrofa	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	LB [auth Ac]	70	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for K7GR43 (Sus scrofa) Explore K7GR43 Go to UniProtKB: K7GR43
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UniProt Group	K7GR43
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	EC [auth Av], MB [auth Ad], XB [auth Ao], YB [auth Ap]	43	Sus scrofa	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	NB [auth Ae]	116	Sus scrofa	Mutation(s): 0
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	OB [auth Af]	128	Sus scrofa	Mutation(s): 0
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	PB [auth Ag]	141	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for I3LGM4 (Sus scrofa) Explore I3LGM4 Go to UniProtKB: I3LGM4
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UniProt Group	I3LGM4
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	SB [auth Aj]	176	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for I3LDC3 (Sus scrofa) Explore I3LDC3 Go to UniProtKB: I3LDC3
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UniProt Group	I3LDC3
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	TB [auth Ak]	178	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for K7GSE5 (Sus scrofa) Explore K7GSE5 Go to UniProtKB: K7GSE5
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UniProt Group	K7GSE5
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	UB [auth Al]	122	Sus scrofa	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C1	VB [auth Am]	76	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1RRC9 (Sus scrofa) Explore F1RRC9 Go to UniProtKB: F1RRC9
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UniProt Group	F1RRC9
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	WB [auth An]	172	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SLR1 (Sus scrofa) Explore F1SLR1 Go to UniProtKB: F1SLR1
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UniProt Group	F1SLR1
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	BC [auth As], FC [auth Aw], ZB [auth Aq]	76	Sus scrofa	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	AC [auth Ar]	34	Sus scrofa	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	CC [auth At]	17	Sus scrofa	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment	DC [auth Au]	13	Sus scrofa	Mutation(s): 0
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Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain AD [auth y] SDF format, chain ZC [auth y] MOL2 format, chain AD [auth y] MOL2 format, chain ZC [auth y] mmCIF format, chain AD [auth y] mmCIF format, chain ZC [auth y]	AD [auth y], ZC [auth y]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AD [auth y] Focus chain ZC [auth y] Interactions & Density Focus chain AD [auth y] Focus chain ZC [auth y]
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain XC [auth p] MOL2 format, chain XC [auth p] mmCIF format, chain XC [auth p]	XC [auth p]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain XC [auth p] Interactions & Density Focus chain XC [auth p]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain IC [auth D] SDF format, chain MC [auth P] MOL2 format, chain IC [auth D] MOL2 format, chain MC [auth P] mmCIF format, chain IC [auth D] mmCIF format, chain MC [auth P]	IC [auth D], MC [auth P]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain IC [auth D] Focus chain MC [auth P] Interactions & Density Focus chain IC [auth D] Focus chain MC [auth P]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain GC [auth C] SDF format, chain HC [auth C] SDF format, chain KC [auth O] SDF format, chain LC [auth O] MOL2 format, chain GC [auth C] MOL2 format, chain HC [auth C] MOL2 format, chain KC [auth O] MOL2 format, chain LC [auth O] mmCIF format, chain GC [auth C] mmCIF format, chain HC [auth C] mmCIF format, chain KC [auth O] mmCIF format, chain LC [auth O]	GC [auth C], HC [auth C], KC [auth O], LC [auth O]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain GC [auth C] Focus chain HC [auth C] Focus chain KC [auth O] Focus chain LC [auth O] Interactions & Density Focus chain GC [auth C] Focus chain HC [auth C] Focus chain KC [auth O] Focus chain LC [auth O]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain VC [auth c] MOL2 format, chain VC [auth c] mmCIF format, chain VC [auth c]	VC [auth c]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain VC [auth c] Interactions & Density Focus chain VC [auth c]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain OC [auth Y] SDF format, chain PC [auth Y] SDF format, chain RC [auth a] SDF format, chain SC [auth b] SDF format, chain TC [auth b] SDF format, chain UC [auth c] MOL2 format, chain OC [auth Y] MOL2 format, chain PC [auth Y] MOL2 format, chain RC [auth a] MOL2 format, chain SC [auth b] MOL2 format, chain TC [auth b] MOL2 format, chain UC [auth c] mmCIF format, chain OC [auth Y] mmCIF format, chain PC [auth Y] mmCIF format, chain RC [auth a] mmCIF format, chain SC [auth b] mmCIF format, chain TC [auth b] mmCIF format, chain UC [auth c]	OC [auth Y] PC [auth Y] RC [auth a] SC [auth b] TC [auth b] OC [auth Y], PC [auth Y], RC [auth a], SC [auth b], TC [auth b], UC [auth c]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain OC [auth Y] Focus chain PC [auth Y] Focus chain RC [auth a] Focus chain SC [auth b] Focus chain TC [auth b] Focus chain UC [auth c] Interactions & Density Focus chain OC [auth Y] Focus chain PC [auth Y] Focus chain RC [auth a] Focus chain SC [auth b] Focus chain TC [auth b] Focus chain UC [auth c]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain JC [auth E] SDF format, chain NC [auth Q] SDF format, chain QC [auth Y] SDF format, chain WC [auth d] MOL2 format, chain JC [auth E] MOL2 format, chain NC [auth Q] MOL2 format, chain QC [auth Y] MOL2 format, chain WC [auth d] mmCIF format, chain JC [auth E] mmCIF format, chain NC [auth Q] mmCIF format, chain QC [auth Y] mmCIF format, chain WC [auth d]	JC [auth E], NC [auth Q], QC [auth Y], WC [auth d]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain JC [auth E] Focus chain NC [auth Q] Focus chain QC [auth Y] Focus chain WC [auth d] Interactions & Density Focus chain JC [auth E] Focus chain NC [auth Q] Focus chain QC [auth Y] Focus chain WC [auth d]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain YC [auth 3] MOL2 format, chain YC [auth 3] mmCIF format, chain YC [auth 3]	YC [auth 3]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain YC [auth 3] Interactions & Density Focus chain YC [auth 3]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain BD [auth y] SDF format, chain DD [auth z] SDF format, chain ED [auth z] MOL2 format, chain BD [auth y] MOL2 format, chain DD [auth z] MOL2 format, chain ED [auth z] mmCIF format, chain BD [auth y] mmCIF format, chain DD [auth z] mmCIF format, chain ED [auth z]	BD [auth y], DD [auth z], ED [auth z]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BD [auth y] Focus chain DD [auth z] Focus chain ED [auth z] Interactions & Density Focus chain BD [auth y] Focus chain DD [auth z] Focus chain ED [auth z]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CD [auth y] MOL2 format, chain CD [auth y] mmCIF format, chain CD [auth y]	CD [auth y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CD [auth y] Interactions & Density Focus chain CD [auth y]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	2.1
MODEL REFINEMENT	PHENIX	1.9

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31030020 and 31170679
Ministry of Science and Technology	China	2012CB911101

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-04-12
Changes: Refinement description
Version 1.2: 2024-10-09
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 5GPN | pdb_00005gpn

Architecture of mammalian respirasome

The architecture of the mammalian respirasome.

Entity ID: 1

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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5GPN | pdb_00005gpn