6ZK9

Peripheral domain of open complex I during turnover


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 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 coupling mechanism of mammalian respiratory complex I.

Kampjut, D.Sazanov, L.A.

(2020) Science 370

  • DOI: https://doi.org/10.1126/science.abc4209
  • Primary Citation of Related Structures:  
    6ZK9, 6ZKA, 6ZKB, 6ZKC, 6ZKD, 6ZKE, 6ZKF, 6ZKG, 6ZKH, 6ZKI, 6ZKJ, 6ZKK, 6ZKL, 6ZKM, 6ZKN, 6ZKO, 6ZKP, 6ZKQ, 6ZKR, 6ZKS, 6ZKT, 6ZKU, 6ZKV

  • PubMed Abstract: 

    Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.


  • Organizational Affiliation

    IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA [auth 1]464Ovis ariesMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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UniProt GroupW5PUX0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 24 kDa subunitB [auth 2]246Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NRY1 (Ovis aries)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S1C [auth 3]727Ovis ariesMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 49 kDa subunitD [auth 4]463Ovis ariesMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S3E [auth 5]266Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, PSST subunitF [auth 6]223Ovis ariesMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, TYKY subunitG [auth 9]217Ovis ariesMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 10 kDa subunitH [auth a]109Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 13 kDa subunitI [auth b]124Ovis ariesMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialJ [auth c]170Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9K [auth d]380Ovis ariesMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2L [auth e]99Ovis ariesMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B13 subunitM [auth f]116Ovis ariesMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A6N [auth g]140Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5a subunitO [auth h]114Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P0I2 (Ovis aries)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12P [auth i]145Ovis ariesMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinQ [auth j]157Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B16.6 subunitR [auth q]144Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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JA [auth h]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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BA [auth 6],
DA [auth 9]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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CA [auth 6],
KA [auth i]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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

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

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

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AA [auth 6]
EA [auth 9]
FA [auth 9]
S [auth 1]
W [auth 3]
AA [auth 6],
EA [auth 9],
FA [auth 9],
S [auth 1],
W [auth 3],
X [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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

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

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Z [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
D [auth 4]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
AYA
Query on AYA
O [auth h]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.12
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union665385
European CommissionEuropean Union653706

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references