7ZCI

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 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

A universal coupling mechanism of respiratory complex I.

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

(2022) Nature 609: 808-814

  • DOI: https://doi.org/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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FA [auth F]445Escherichia coliMutation(s): 0 
EC: 7.1.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit EB [auth E]166Escherichia coliMutation(s): 0 
EC: 7.1.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseC [auth G]908Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DD [auth C]596Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BE [auth B]220Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]180Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AH [auth A]147Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit LI [auth L]613Escherichia coliMutation(s): 0 
EC: 1.6.5.11 (PDB Primary Data), 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit MJ [auth M]509Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NK [auth N]485Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KL [auth K]100Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JM [auth J]184Escherichia coliMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE
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AA [auth H],
CA [auth L],
DA [auth L],
EA [auth L],
FA [auth L],
AA [auth H],
CA [auth L],
DA [auth L],
EA [auth L],
FA [auth L],
HA [auth L],
IA [auth L],
JA [auth M],
KA [auth M],
MA [auth N],
OA [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N		 Ligand Interaction
NAI
Query on NAI
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P [auth F]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N		 Ligand Interaction
FMN
Query on FMN
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O [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
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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
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BA [auth A],
GA [auth L],
LA [auth N],
NA [auth N],
Z [auth H]		EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
FES
Query on FES
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Q [auth E],
U [auth G]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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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
  • Version 1.2: 2022-10-05
    Changes: Database references