7ZDP

Complex I from Ovis aries at pH9, Open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-49kDA [auth 4]463Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6P3DZ89 (Ovis aries)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3B [auth A]115Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1C [auth H]318Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6D [auth J]175Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LE [auth K]98Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5F [auth L]606Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4G [auth M]459Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2H [auth N]347Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B14.7I [auth V]140Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8N7XJ91 (Ovis aries)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-SGDHJ [auth W]139Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinK [auth X],
SA [auth j]
157Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8L [auth Y]171Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-PDSWM [auth Z]171Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialN [auth k]320Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5O [auth l]105Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B9P [auth m]80Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B12Q [auth n]79Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2R [auth o]120Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4S [auth p]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13T [auth q]144Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B17 subunitU [auth r]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PZE3 (Ovis aries)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B18V [auth s]122Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B22W [auth t]177Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A6P3E749 (Ovis aries)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-AGGGX [auth u]65Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialY [auth v]155Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-ESSSZ [auth w]101Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-KFYIAA [auth x]49Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-MNLLBA [auth y]50Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-MWFECA [auth z]70Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialDA [auth 1]430Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialEA [auth 2]213Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialFA [auth 3]688Ovis ariesMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-30kDGA [auth 5]208Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-20kDHA [auth 6]156Ovis ariesMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-23kDIA [auth 9]176Ovis ariesMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-9kDJA [auth a]44Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialKA [auth b]95Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialLA [auth c]126Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9MA [auth d]380Ovis ariesMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2NA [auth e]86Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I subunit B13OA [auth f]113Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B14PA [auth g]114Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
Explore W5QC06 
Go to UniProtKB:  W5QC06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5QC06
Sequence Annotations
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  • Reference Sequence
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5a subunitQA [auth h]114Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P0I2 (Ovis aries)
Explore W5P0I2 
Go to UniProtKB:  W5P0I2
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UniProt GroupW5P0I2
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  • Reference Sequence
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12RA [auth i]145Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8N7XJ18 (Ovis aries)
Explore A0A8N7XJ18 
Go to UniProtKB:  A0A8N7XJ18
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8N7XJ18
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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IB [auth d]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAI
Query on NAI

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YA [auth 1]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
ZMP
Query on ZMP

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JB [auth j],
TA [auth X]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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XA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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AB [auth 3]
BB [auth 3]
EB [auth 6]
FB [auth 9]
GB [auth 9]
AB [auth 3],
BB [auth 3],
EB [auth 6],
FB [auth 9],
GB [auth 9],
WA [auth 1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
AMP
Query on AMP

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UA [auth k]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
MYR
Query on MYR

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VA [auth s]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FES
Query on FES

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CB [auth 3],
ZA [auth 2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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HB [auth b]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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DB [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
A [auth 4]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME
E [auth K]L-PEPTIDE LINKINGC6 H11 N O3 SMET
AYA
Query on AYA
I [auth V]L-PEPTIDE LINKINGC5 H9 N O3ALA
SEP
Query on SEP
N [auth k]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101020697

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