7Z83

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A universal coupling mechanism of respiratory complex I.

Kravchuk, V.Petrova, O.Kampjut, D.Wojciechowska-Bason, A.Breese, Z.Sazanov, L.

(2022) Nature 

  • DOI: 10.1038/s41586-022-05199-7
  • Primary Citation of Related Structures:  
    7P61, 7P62, 7P63, 7P64, 7P69, 7P7C, 7P7E, 7P7J, 7P7K, 7P7L, 7P7M, 7Z7R, 7Z7S, 7Z7T, 7Z7V, 7Z80, 7Z83, 7Z84, 7ZC5, 7ZCI, 7ZD6, 7ZDH, 7ZDJ, 7ZDM, 7ZDP, 7ZEB

  • PubMed Abstract: 
  • Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria 1 . Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane 2 , but the coupling mechanism remains contentious ...

    Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria 1 . Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane 2 , but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues 3 , EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.


    Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg, Austria. sazanov@ist.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FA [auth F]445Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
UniProt
Find proteins for A0A037YNA7 (Escherichia coli)
Explore A0A037YNA7 
Go to UniProtKB:  A0A037YNA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A037YNA7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit EB [auth E]166Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for A0A829CRH1 (Escherichia coli MP021552.8)
Explore A0A829CRH1 
Go to UniProtKB:  A0A829CRH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A829CRH1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseC [auth G]908Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CDD [auth C]600Escherichia coli BL21(DE3)Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BE [auth B]220Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]180Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V1DR98 (Escherichia coli O145:NM)
Explore A0A4V1DR98 
Go to UniProtKB:  A0A4V1DR98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V1DR98
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for E6BKM7 (Escherichia coli MS 85-1)
Explore E6BKM7 
Go to UniProtKB:  E6BKM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6BKM7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AH [auth A]147Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A358FP87 (Shigella sp)
Explore A0A358FP87 
Go to UniProtKB:  A0A358FP87
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A358FP87
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit LI [auth L]613Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.99.5
Membrane Entity: Yes 
UniProt
Find proteins for A0A1V3W1N5 (Escherichia coli)
Explore A0A1V3W1N5 
Go to UniProtKB:  A0A1V3W1N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V3W1N5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit MJ [auth M]509Escherichia coli BL21(DE3)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C3T2G7 (Escherichia coli)
Explore C3T2G7 
Go to UniProtKB:  C3T2G7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3T2G7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NK [auth N]485Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for E2QPD7 (Escherichia coli)
Explore E2QPD7 
Go to UniProtKB:  E2QPD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE2QPD7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KL [auth K]100Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A7U9LRT0 (Escherichia coli O145:H28)
Explore A0A7U9LRT0 
Go to UniProtKB:  A0A7U9LRT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U9LRT0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JM [auth J]184Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3MIP2 (Escherichia coli O7:K1 (strain IAI39 / ExPEC))
Explore A0A0H3MIP2 
Go to UniProtKB:  A0A0H3MIP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3MIP2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
BA [auth L],
CA [auth L],
DA [auth L],
EA [auth L],
GA [auth M],
BA [auth L],
CA [auth L],
DA [auth L],
EA [auth L],
GA [auth M],
HA [auth M],
KA [auth J],
LA [auth J],
Z [auth H]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NAI
Query on NAI

Download Ideal Coordinates CCD File 
P [auth F]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
O [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
N [auth F],
R [auth G],
S [auth G],
T [auth G],
W [auth B],
N [auth F],
R [auth G],
S [auth G],
T [auth G],
W [auth B],
X [auth I],
Y [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth H],
FA [auth M],
IA [auth N],
JA [auth N]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
Q [auth E],
U [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedAustria25541

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references