9GAE | pdb_00009gae

Respiratory supercomplex CI1-CIII2-CIV2 from alphaproteobacterium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Entire structure of ancestral alphaproteobacterial complex I reveals the mechanism to prevent its deactivation

Yaikhomba, M.Hirst, J.Croll, T.I.Spikes, T.E.

To be published.

Macromolecule Content 

  • Total Structure Weight: 1,284.5 kDa 
  • Atom Count: 82,894 
  • Modeled Residue Count: 9,509 
  • Deposited Residue Count: 10,533 
  • Unique protein chains: 27

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit A121Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit B175Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C208Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit D412Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit E239Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit F431Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase674Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit H345Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit I163Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit J199Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit K101Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit L703Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit M513Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit N499Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent epimerase/dehydrataseO [auth P]330Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1AZB0 (Paracoccus denitrificans (strain Pd 1222))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
ETC complex I subunit conserved regionP [auth Q]103Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger CHCC-type domain-containing proteinQ [auth R]62Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-L-isoaspartate O-methyltransferaseR [auth Z]217Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bS [auth a],
V [auth d]
440Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1B4F3 (Paracoccus denitrificans (strain Pd 1222))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1T [auth b],
W [auth e]
450Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitU [auth c],
X [auth f]
195Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1.8
UniProt
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1CA [auth k],
Y [auth g]
558Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1.9
UniProt
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2DA [auth l],
Z [auth h]
298Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1.9
UniProt
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome-c oxidaseAA [auth i],
EA [auth m]
274Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for A1BA37 (Paracoccus denitrificans (strain Pd 1222))
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Reference Sequence
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Aa3 type cytochrome c oxidase subunit IVBA [auth j],
FA [auth n]
66Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1AZ52 (Paracoccus denitrificans (strain Pd 1222))
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Reference Sequence
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c, class IGA [auth o],
HA [auth p]
176Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 17.2 kD subunitIA [auth q]124Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1B1H8 (Paracoccus denitrificans (strain Pd 1222))
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Reference Sequence

Small Molecules

Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



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TD [auth d]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
T7X

Query on T7X



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HF [auth g],
JB [auth J]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
U10

Query on U10



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CD [auth a],
DD [auth a],
NA [auth B],
WD [auth d],
YD [auth d]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
HEA
(Subject of Investigation/LOI)

Query on HEA



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CF [auth g],
PG [auth k],
QG [auth k],
YE [auth g]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
P5S

Query on P5S



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ED [auth a],
FB [auth I],
WB [auth L]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
PC1

Query on PC1



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AG [auth i]
AH [auth l]
BE [auth d]
DG [auth i]
DH [auth m]
AG [auth i],
AH [auth l],
BE [auth d],
DG [auth i],
DH [auth m],
EF [auth g],
GC [auth M],
HC [auth M],
ID [auth a],
IE [auth d],
JC [auth N],
JD [auth b],
JG [auth j],
KC [auth N],
LF [auth h],
LH [auth m],
MC [auth N],
MD [auth b],
MH [auth m],
OA [auth D],
OE [auth f],
OH [auth m],
PD [auth c],
QB [auth L],
QH [auth n],
RG [auth k],
SC [auth a],
UG [auth k],
XA [auth H],
XG [auth l],
YA [auth H],
YC [auth a],
YF [auth i],
ZB [auth M],
ZG [auth l]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PGT

Query on PGT



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AC [auth M]
BB [auth H]
FD [auth a]
IB [auth J]
KA [auth A]
AC [auth M],
BB [auth H],
FD [auth a],
IB [auth J],
KA [auth A],
MB [auth J],
NB [auth K],
NC [auth N],
OC [auth P],
RB [auth L],
UE [auth g],
UH [auth q]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
3PE

Query on 3PE



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AB [auth H]
AD [auth a]
BG [auth i]
CB [auth H]
CE [auth d]
AB [auth H],
AD [auth a],
BG [auth i],
CB [auth H],
CE [auth d],
DB [auth H],
EH [auth m],
FF [auth g],
FH [auth m],
GH [auth m],
HE [auth d],
HG [auth i],
HH [auth m],
JA [auth A],
KE [auth e],
KF [auth h],
KH [auth m],
ND [auth c],
NE [auth e],
OG [auth k],
PB [auth L],
PH [auth m],
QC [auth P],
QF [auth h],
RH [auth n],
SB [auth L],
TB [auth L],
TC [auth a],
TE [auth g],
TH [auth p],
UC [auth a],
VB [auth L],
VD [auth d],
WF [auth i],
XF [auth i],
ZA [auth H],
ZC [auth a],
ZE [auth g],
ZF [auth i]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH

Query on 3PH



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AE [auth d]
BC [auth M]
BD [auth a]
BH [auth m]
CC [auth M]
AE [auth d],
BC [auth M],
BD [auth a],
BH [auth m],
CC [auth M],
DC [auth M],
DF [auth g],
EB [auth H],
EC [auth M],
EG [auth i],
FE [auth d],
IG [auth i],
JH [auth m],
LC [auth N],
LG [auth j],
MG [auth k],
OB [auth L],
PC [auth P],
QE [auth f],
RF [auth i],
SD [auth c],
SE [auth f],
SG [auth k],
SH [auth o],
TF [auth i],
UB [auth L],
UD [auth d],
UF [auth i],
VC [auth a],
VE [auth g],
XB [auth L],
XC [auth a],
YB [auth L]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
HEC
(Subject of Investigation/LOI)

Query on HEC



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KD [auth b],
ME [auth e]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



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GD [auth a],
GE [auth d],
WC [auth a],
ZD [auth d]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DU0

Query on DU0



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CH [auth m]
DE [auth d]
EE [auth d]
FC [auth M]
FG [auth i]
CH [auth m],
DE [auth d],
EE [auth d],
FC [auth M],
FG [auth i],
GG [auth i],
HD [auth a],
IC [auth M],
IF [auth g],
JF [auth g],
KB [auth J],
KG [auth j],
LA [auth A],
LB [auth J],
LE [auth e],
MF [auth h],
NF [auth h],
NH [auth m],
OD [auth c],
PE [auth f],
PF [auth h],
RD [auth c],
SF [auth i],
TG [auth k],
VF [auth i],
WA [auth H],
WE [auth g],
XD [auth d],
XE [auth g]
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
C32 H52 O5
GFDJQXOBWHMOSQ-LEZUHYJESA-N
FMN
(Subject of Investigation/LOI)

Query on FMN



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SA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



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GB [auth I]
HB [auth I]
MA [auth B]
RA [auth F]
UA [auth G]
GB [auth I],
HB [auth I],
MA [auth B],
RA [auth F],
UA [auth G],
VA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



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QA [auth E],
QD [auth c],
RE [auth f],
TA [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA

Query on CUA



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OF [auth h],
YG [auth l]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN



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CG [auth i],
IH [auth m],
RC [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



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BF [auth g],
VG [auth k]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MN

Query on MN



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GF [auth g],
WG [auth k]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



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AF [auth g],
JE [auth e],
LD [auth b],
NG [auth k],
PA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  2 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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 and MC_UU_00028/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release