8Q45 | pdb_00008q45

Inward-facing, closed proteoliposome complex I at 2.7 A. Initially purified in LMNG.

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Bos taurus
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2023-08-05 Released: 2024-06-05 
  • Deposition Author(s): Grba, D.N., Hirst, J.
  • Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I.

Grba, D.N.Wright, J.J.Yin, Z.Fisher, W.Hirst, J.

(2024) Science 384: 1247-1253

  • DOI: https://doi.org/10.1126/science.ado2075
  • Primary Citation Related Structures: 
    8Q0A, 8Q0F, 8Q0J, 8Q0M, 8Q0O, 8Q0Q, 8Q1P, 8Q1U, 8Q1Y, 8Q25, 8Q45, 8Q46, 8Q47, 8Q48, 8Q49, 8Q4A

  • PubMed Abstract: 

    Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.


  • Organizational Affiliation
    • Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.

Macromolecule Content 

  • Total Structure Weight: 1,107.16 kDa 
  • Atom Count: 70,020 
  • Modeled Residue Count: 8,293 
  • Deposited Residue Count: 9,213 
  • Unique protein chains: 44

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3115Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03898 (Bos taurus)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial216Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P42026 (Bos taurus)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial266Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P23709 (Bos taurus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial463Bos taurusMutation(s): 1 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P17694 (Bos taurus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial249Bos taurusMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P04394 (Bos taurus)
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UniProt GroupP04394
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial464Bos taurusMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P25708 (Bos taurus)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial727Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P15690 (Bos taurus)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1318Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03887 (Bos taurus)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial212Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P42028 (Bos taurus)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6175Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P03924 (Bos taurus)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L98Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P03902 (Bos taurus)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5606Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03920 (Bos taurus)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03910 (Bos taurus)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2347Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03892 (Bos taurus)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial343Bos taurusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P34942 (Bos taurus)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial380Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial175Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q02375 (Bos taurus)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial124Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23934 (Bos taurus)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 299Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q02370 (Bos taurus)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrial
T, U
156Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P52505 (Bos taurus)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5116Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23935 (Bos taurus)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8172Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P42029 (Bos taurus)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11141Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8HXG6 (Bos taurus)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13144Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q95KV7 (Bos taurus)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q02377 (Bos taurus)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3BA [auth b]84Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth c]76Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth d]120Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q02827 (Bos taurus)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth e]106Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth f]57Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth g]154Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q8HXG5 (Bos taurus)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialHA [auth h]189Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6IA [auth i]128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialJA [auth j]108Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3KA [auth k]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialLA [auth l]186Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth m]129Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth n]179Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth o]137Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10PA [auth p]176Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth q]145Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7RA [auth r]113Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialSA [auth s]109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
GC [auth M]
JC [auth N]
JD [auth d]
PC [auth P]
SB [auth J]
GC [auth M],
JC [auth N],
JD [auth d],
PC [auth P],
SB [auth J],
SD [auth i],
XC [auth X],
YB [auth L],
YD [auth q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10

Query on U10



Download:Ideal Coordinates CCD File
CB [auth D]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1

Query on PC1



Download:Ideal Coordinates CCD File
BB [auth B]
DC [auth L]
EC [auth L]
IC [auth M]
KB [auth H]
BB [auth B],
DC [auth L],
EC [auth L],
IC [auth M],
KB [auth H],
LD [auth d],
MB [auth H],
OD [auth g],
PB [auth I],
QB [auth I],
QC [auth P],
QD [auth h],
TB [auth J],
UA [auth A],
VA [auth A],
ZD [auth q]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
AC [auth L]
AD [auth Y]
AE [auth q]
BD [auth Y]
CC [auth L]
AC [auth L],
AD [auth Y],
AE [auth q],
BD [auth Y],
CC [auth L],
CD [auth Y],
DD [auth Y],
FD [auth Y],
GD [auth Z],
HC [auth M],
HD [auth a],
ID [auth b],
KC [auth N],
KD [auth d],
LB [auth H],
ND [auth g],
RB [auth I],
RC [auth P],
TA [auth A],
TC [auth P],
TD [auth j],
UB [auth J],
UD [auth m],
VB [auth J],
VD [auth m],
WA [auth A],
XA [auth A],
XB [auth J],
XD [auth p],
YC [auth Y],
ZB [auth L],
ZC [auth Y]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP

Query on NDP



Download:Ideal Coordinates CCD File
OC [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PLC

Query on PLC



Download:Ideal Coordinates CCD File
AB [auth B]
BC [auth L]
ED [auth Y]
MD [auth d]
NC [auth O]
AB [auth B],
BC [auth L],
ED [auth Y],
MD [auth d],
NC [auth O],
PD [auth h],
SC [auth P],
WB [auth J],
YA [auth A]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
EHZ

Query on EHZ



Download:Ideal Coordinates CCD File
VC [auth T],
WC [auth U]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
DGT

Query on DGT



Download:Ideal Coordinates CCD File
LC [auth O]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
EB [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
CHD

Query on CHD



Download:Ideal Coordinates CCD File
RD [auth i]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
FB [auth F]
GB [auth G]
HB [auth G]
NB [auth I]
OB [auth I]
FB [auth F],
GB [auth G],
HB [auth G],
NB [auth I],
OB [auth I],
ZA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MYR

Query on MYR



Download:Ideal Coordinates CCD File
WD [auth o]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
DB [auth E],
IB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
FC [auth M],
UC [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
JB [auth G]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
MC [auth O]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
AYA
Query on AYA
Y
L-PEPTIDE LINKINGC5 H9 N O3ALA
SAC
Query on SAC
IA [auth i]L-PEPTIDE LINKINGC5 H9 N O4SER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONRELION4.0-beta

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00028/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references