6ZKT

Deactive complex I, open2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinB [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
NADH-ubiquinone oxidoreductase chain 3H [auth A]115Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1I [auth H]318Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6175Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L98Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5606Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2347Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinO [auth V]141Ovis ariesMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B5P [auth W]189Ovis ariesMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinCA [auth j],
Q [auth X]
157Ovis ariesMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8R [auth Y]172Ovis ariesMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, PDSW subunitS [auth Z]175Ovis ariesMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 10 kDa subunitT [auth a]109Ovis ariesMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 13 kDa subunitU [auth b]124Ovis ariesMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialV [auth c]170Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9W [auth d]380Ovis ariesMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2X [auth e]99Ovis ariesMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinY [auth f]116Ovis ariesMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A6Z [auth g]140Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinAA [auth h]114Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12BA [auth i]145Ovis ariesMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialDA [auth k]355Ovis ariesMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S5EA [auth l]106Ovis ariesMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A3FA [auth m]84Ovis ariesMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B3GA [auth n]98Ovis ariesMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2HA [auth o]122Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4IA [auth p]130Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B16.6 subunitJA [auth q]144Ovis ariesMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinKA [auth r]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B7LA [auth s]137Ovis ariesMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B9MA [auth t]179Ovis ariesMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2NA [auth u]108Ovis ariesMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialOA [auth v]186Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinPA [auth w]154Ovis ariesMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, KFYI subunitQA [auth x]76Ovis ariesMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, MNLL subunitRA [auth y]58Ovis ariesMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, MWFE subunitSA [auth z]70Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AC [auth o]
KB [auth L]
NB [auth M]
OB [auth M]
RB [auth W]
AC [auth o],
KB [auth L],
NB [auth M],
OB [auth M],
RB [auth W],
WB [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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BB [auth 6]
CC [auth w]
FB [auth A]
GB [auth H]
JB [auth L]
BB [auth 6],
CC [auth w],
FB [auth A],
GB [auth H],
JB [auth L],
MB [auth M]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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CB [auth 6]
HB [auth H]
IB [auth L]
LB [auth L]
PB [auth N]
CB [auth 6],
HB [auth H],
IB [auth L],
LB [auth L],
PB [auth N],
QB [auth N],
XB [auth i],
ZB [auth m]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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

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SB [auth X],
VB [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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UA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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

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

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BC [auth s]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FES
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VA [auth 2],
YA [auth 3]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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