7O37 | pdb_00007o37

Murine supercomplex CIII2CIV in the assembled locked conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure and assembly of the mammalian mitochondrial supercomplex CIII 2 CIV.

Vercellino, I.Sazanov, L.A.

(2021) Nature 598: 364-367

  • DOI: https://doi.org/10.1038/s41586-021-03927-z
  • Primary Citation Related Structures: 
    7O37, 7O3C, 7O3E, 7O3H

  • PubMed Abstract: 

    The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes 1 , whose precise role is debated. Supercomplexes CIII 2 CIV 1-2 (refs. 2,3 ), CICIII 2 (ref. 4 ) and CICIII 2 CIV (respirasome) 5-10 exist in mammals, but in contrast to CICIII 2 and the respirasome, to date the only known eukaryotic structures of CIII 2 CIV 1-2 come from Saccharomyces cerevisiae 11,12 and plants 13 , which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII 2 CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII 2 CIV from the CIII 2 precursor to the final CIII 2 CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14 ) deep into CIII 2 , while its C terminus is integrated into CIV. Our structures (which include CICIII 2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII 2 CIV and has no role in the assembly of the respirasome. We show that CIII 2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII 2 , explaining the presence of one copy of CIV in CIII 2 CIV in mammals. Finally, we show that CIII 2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII 2 CIV in fine tuning the efficiency of electron transfer in the electron transport chain.


  • Organizational Affiliation
    • IV & LAS: IST Austria, Klosterneuburg, Austria.

Macromolecule Content 

  • Total Structure Weight: 717.85 kDa 
  • Atom Count: 48,610 
  • Modeled Residue Count: 5,970 
  • Deposited Residue Count: 6,120 
  • Unique protein chains: 24

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
K [auth L]
446Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:107876
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
L [auth M]
439Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9DB77 (Mus musculus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bC,
M [auth N]
381Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
N [auth O]
241Mus musculusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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IMPC:  MGI:1913695
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
O [auth P]
196Mus musculusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR68 (Mus musculus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
P [auth Q]
110Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914780
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G,
Q [auth R]
81Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:107807
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH,
R [auth S]
76Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913826
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I [auth J],
S [auth U]
63Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913402
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10J [auth K],
T [auth V]
56Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPX8 (Mus musculus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9U [auth T]78Mus musculusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR68 (Mus musculus)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cox7a2l proteinV [auth I]113Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:106015
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1W [auth a]514Mus musculusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2X [auth b]227Mus musculusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3Y [auth c]261Mus musculusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialZ [auth d]147Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:88473
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialAA [auth e]109Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialBA [auth f]99Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P19536 (Mus musculus)
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IMPC:  MGI:88475
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UniProt GroupP19536
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialCA [auth g]85Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1DA [auth h]85Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P56391 (Mus musculus)
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IMPC:  MGI:107460
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CEA [auth i]75Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialFA [auth k]56Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialGA [auth l]47Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P17665 (Mus musculus)
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IMPC:  MGI:103226
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialHA [auth m]46Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
DB [auth O]
HB [auth R]
JA [auth A]
NA [auth D]
TA [auth G]
DB [auth O],
HB [auth R],
JA [auth A],
NA [auth D],
TA [auth G],
ZA [auth L]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL

Query on TGL



Download:Ideal Coordinates CCD File
WA [auth G]TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA

Query on HEA



Download:Ideal Coordinates CCD File
MB [auth a],
NB [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1

Query on PC1



Download:Ideal Coordinates CCD File
JB [auth U],
PB [auth a],
RA [auth E],
VA [auth G],
XA [auth G]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
CB [auth N]
EB [auth O]
IA [auth A]
IB [auth R]
MA [auth C]
CB [auth N],
EB [auth O],
IA [auth A],
IB [auth R],
MA [auth C],
OA [auth D],
OB [auth a],
QB [auth a],
SA [auth F],
SB [auth b],
UA [auth G],
UB [auth b],
VB [auth c],
XB [auth g],
YA [auth L],
YB [auth k]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC

Query on HEC



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FB [auth O],
PA [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



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AB [auth N],
BB [auth N],
KA [auth C],
LA [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES

Query on FES



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GB [auth P],
QA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA

Query on CUA



Download:Ideal Coordinates CCD File
TB [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
WB [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
KB [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG

Query on MG



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RB [auth b]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
LB [auth a]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionAustria754411

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Data collection, Database references
  • Version 1.2: 2021-10-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary