6HU9

III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.

Hartley, A.M.Lukoyanova, N.Zhang, Y.Cabrera-Orefice, A.Arnold, S.Meunier, B.Pinotsis, N.Marechal, A.

(2019) Nat. Struct. Mol. Biol. 26: 78-83

  • DOI: 10.1038/s41594-018-0172-z

  • PubMed Abstract: 
  • Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc <sub>1 </su ...

    Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc 1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III 2 IV 2 SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.


    Organizational Affiliation

    Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Institute of Structural and Molecular Biology, University College London, London, UK.,Institute of Structural and Molecular Biology, Birkbeck College, London, UK. a.marechal@ucl.ac.uk.,Institute of Structural and Molecular Biology, University College London, London, UK. a.marechal@ucl.ac.uk.,Institute of Structural and Molecular Biology, Birkbeck College, London, UK.,Institute of Structural and Molecular Biology, Birkbeck College, London, UK. n.pinotsis@mail.cryst.bbk.ac.uk.,Institute for Integrative Biology of the Cell, Université Paris-Saclay, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A, L
431Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COR1 (QCR1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrial
B, M
352Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR2 (COR2, UCR2)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, N
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COB (CYTB)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial
D, O
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CYT1 (CTC1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07143
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, P
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RIP1
EC: 7.1.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08067
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6
F, Q
147Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR6 (UCR6)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00127
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
G, R
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR7 (CRO1, UCR7)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8
H, S
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9
I, T
66Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR9 (UCR9)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 10
J, U
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR10
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P37299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P37299
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
a, m
534Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX1 (OXI3)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00401
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
b, n
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX2 (OXI1)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00410
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
c, o
269Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX3 (OXI2)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00420
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4, mitochondrial
d, p
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX4
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04037
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide 5A, mitochondrial
e, q
133Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: COX5A
Go to UniProtKB:  P00424
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6, mitochondrial
f, r
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX6
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00427
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7
g, s
59Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX7
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10174
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIII, mitochondrial
h, t
47Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX8
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P04039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04039
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7A
i, u
55Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX9
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07255
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6B
j, v
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX12
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for Q01519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01519
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6A, mitochondrial
k, w
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX13
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P32799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32799
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Cox26
l, x
66Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q2V2P9
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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a, m
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

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d, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CDL
Query on CDL

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C, E, H, L, O, P, S
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PEF
Query on PEF

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A, a, b, c, C, D, E, e, h, H, m, n, N, o, O, P, q, S, t
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
CA
Query on CA

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a, m
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

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b, n
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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E, P
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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a, m
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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C, N
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

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a, m
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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D, O
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PCF
Query on PCF

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C, e, H, I, N, q, S, T
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
UQ6
Query on UQ6

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Download CCD File 
C
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M00936X/1
Wellcome TrustUnited Kingdom105628/Z/14/Z

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-01-09
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references
  • Version 1.3: 2019-01-23
    Type: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Type: Other