7W4N

Deactive state CI from Q1-NADH dataset, Subclass 5

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2021-11-28 Released: 2023-01-25 
  • Deposition Author(s): Gu, J., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The coupling mechanism of mammalian mitochondrial complex I

Gu, J.Liu, T.Guo, R.Zhang, L.Yang, M.

(2022) Nat Struct Mol Biol 29: 172-182


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA433Sus scrofaMutation(s): 0 
Gene Names: NDUFV1
EC: 7.1.1.2
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialB176Sus scrofaMutation(s): 0 
Gene Names: NDUFS8
UniProt
Find proteins for A0A287BDC0 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialC156Sus scrofaMutation(s): 0 
Gene Names: NDUFS7
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth E]115Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth F]86Sus scrofaMutation(s): 0 
Gene Names: NDUFA2
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinF [auth G],
V [auth X]
88Sus scrofaMutation(s): 0 
Gene Names: NDUFAB1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I subunit B13G [auth H]112Sus scrofaMutation(s): 0 
Gene Names: NDUFA5
UniProt
Find proteins for A0A5G2RN85 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B14.5aH [auth I]112Sus scrofaMutation(s): 0 
Gene Names: NDUFA7
UniProt
Find proteins for A0A4X1VLA2 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrialI [auth J]342Sus scrofaMutation(s): 0 
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Find proteins for A0A480QJC4 (Sus scrofa)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-9kDJ [auth K]43Sus scrofaMutation(s): 0 
Gene Names: NDUFV3
UniProt
Find proteins for A0A4X1TFI3 (Sus scrofa)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth L]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for G8IFA6 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialL [auth M]690Sus scrofaMutation(s): 0 
Gene Names: NDUFS1
UniProt
Find proteins for F1SHD7 (Sus scrofa)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12M [auth N]144Sus scrofaMutation(s): 0 
Gene Names: NDUFA12
UniProt
Find proteins for F1SQP4 (Sus scrofa)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialN [auth O]217Sus scrofaMutation(s): 0 
Gene Names: NDUFV2
UniProt
Find proteins for A0A287BG40 (Sus scrofa)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-30kDO [auth P]208Sus scrofaMutation(s): 0 
Gene Names: NDUFS3
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-49kDP [auth Q]430Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JYS1 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Q [auth S]70Sus scrofaMutation(s): 0 
Gene Names: NDUFA1
UniProt
Find proteins for K7GR43 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR [auth T]96Sus scrofaMutation(s): 0 
Gene Names: NDUFS6
UniProt
Find proteins for F1S031 (Sus scrofa)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3S [auth U]83Sus scrofaMutation(s): 0 
Gene Names: NDUFA3
UniProt
Find proteins for A0A4X1VQ42 (Sus scrofa)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11T [auth V]140Sus scrofaMutation(s): 0 
Gene Names: NDUFA11
UniProt
Find proteins for I3LGM4 (Sus scrofa)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B16.6U [auth W]142Sus scrofaMutation(s): 0 
Gene Names: NDUFA13
UniProt
Find proteins for F1S6Q1 (Sus scrofa)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-AGGGW [auth Y]70Sus scrofaMutation(s): 0 
Gene Names: NDUFB2
UniProt
Find proteins for A0A4X1V766 (Sus scrofa)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B12X [auth Z]84Sus scrofaMutation(s): 0 
Gene Names: NDUFB3
UniProt
Find proteins for A0A287AS93 (Sus scrofa)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-SGDHY [auth a]140Sus scrofaMutation(s): 0 
Gene Names: NDUFB5
UniProt
Find proteins for F1SGC6 (Sus scrofa)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B17Z [auth b]126Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q2EN80 (Sus scrofa)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialAA [auth c]156Sus scrofaMutation(s): 0 
Gene Names: NDUFB8
UniProt
Find proteins for F1RWL7 (Sus scrofa)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10BA [auth d]175Sus scrofaMutation(s): 0 
Gene Names: NDUFB10
UniProt
Find proteins for A0A4X1VYV0 (Sus scrofa)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialCA [auth e]107Sus scrofaMutation(s): 0 
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Entity ID: 29
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NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialDA [auth f]49Sus scrofaMutation(s): 0 
Gene Names: NDUFC1
UniProt
Find proteins for A1XQS6 (Sus scrofa)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2EA [auth g]122Sus scrofaMutation(s): 0 
Gene Names: NDUFC2
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 31
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 5FA [auth h]105Sus scrofaMutation(s): 0 
Gene Names: NDUFS5
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2GA [auth i]347Sus scrofaMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
UniProt
Find proteins for O79875 (Sus scrofa)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3HA [auth j]115Sus scrofaMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LIA [auth k]98Sus scrofaMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
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Find proteins for P56632 (Sus scrofa)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5JA [auth l]603Sus scrofaMutation(s): 0 
Gene Names: NADH5ND5
EC: 7.1.1.2
UniProt
Find proteins for Q71K68 (Sus scrofa)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6KA [auth m]175Sus scrofaMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1LA [auth n]56Sus scrofaMutation(s): 0 
Gene Names: NDUFB1
UniProt
Find proteins for F1SD73 (Sus scrofa)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth o]128Sus scrofaMutation(s): 0 
Gene Names: NDUFB4
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Find proteins for A0A4X1T6M0 (Sus scrofa)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth p]178Sus scrofaMutation(s): 0 
Gene Names: NDUFB9
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Find proteins for A0A4X1T0A8 (Sus scrofa)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4OA [auth r]459Sus scrofaMutation(s): 0 
Gene Names: NADH4
EC: 7.1.1.2
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1PA [auth s]318Sus scrofaMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
UniProt
Find proteins for O79874 (Sus scrofa)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8QA [auth u]171Sus scrofaMutation(s): 0 
Gene Names: NDUFA8
UniProt
Find proteins for F1SLR1 (Sus scrofa)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I-B18RA [auth v]124Sus scrofaMutation(s): 0 
Gene Names: NDUFB7
UniProt
Find proteins for F1SCH1 (Sus scrofa)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialSA [auth w]320Sus scrofaMutation(s): 0 
Gene Names: NDUFA10
UniProt
Find proteins for F1SIS9 (Sus scrofa)
Explore F1SIS9 
Go to UniProtKB:  F1SIS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1SIS9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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DB [auth I],
NB [auth a],
PB [auth i],
SB [auth l],
TB [auth l],
DB [auth I],
NB [auth a],
PB [auth i],
SB [auth l],
TB [auth l],
YB [auth r]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ (Subject of Investigation/LOI)
Query on UQ

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ZB [auth s]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
PLX (Subject of Investigation/LOI)
Query on PLX

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BB [auth C],
OB [auth g],
RB [auth j],
XB [auth r]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
 Ligand Interaction
NDP (Subject of Investigation/LOI)
Query on NDP

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EB [auth J]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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AB [auth C],
LB [auth U],
QB [auth i],
UB [auth l],
VB [auth m],
AB [auth C],
LB [auth U],
QB [auth i],
UB [auth l],
VB [auth m],
WB [auth r],
YA [auth B]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
NAI (Subject of Investigation/LOI)
Query on NAI

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VA [auth A]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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CB [auth G],
MB [auth X]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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UA [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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AC [auth w]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4 (Subject of Investigation/LOI)
Query on SF4

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FB [auth M],
GB [auth M],
TA [auth A],
WA [auth B],
XA [auth B],
FB [auth M],
GB [auth M],
TA [auth A],
WA [auth B],
XA [auth B],
ZA [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES (Subject of Investigation/LOI)
Query on FES

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HB [auth M],
JB [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

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KB [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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IB [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
P [auth Q]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504600 and 2016YFA0501100
National Natural Science Foundation of China (NSFC)China31625008
National Natural Science Foundation of China (NSFC)China32030056, 21532004 and 31570733 and 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release