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
  • Primary Citation of Related Structures:  
    6HU9

  • 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 1 (complex III, CIII) ...

    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

    Institute of Structural and Molecular Biology, University College London, London, UK. a.marechal@ucl.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA, K [auth L]431Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COR1QCR1YBL045CYBL0403
Membrane Entity: Yes 
UniProt
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB, L [auth M]352Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR2COR2UCR2YPR191WP9677.6
Membrane Entity: Yes 
UniProt
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC, M [auth N]385Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COBCYTBQ0105
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD, N [auth O]248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CYT1CTC1YOR065WYOR29-16
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, O [auth P]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIP1YEL024W
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F, P [auth Q]147Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR6UCR6YFR033C
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7G, Q [auth R]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR7CRO1UCR7YDR529CD9719.32
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8H, R [auth S]93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR8YJL166WJ0526
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I, S [auth T]66Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR9UCR9YGR183C
Membrane Entity: Yes 
UniProt
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10J, T [auth U]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR10YHR001W-AYHR001BW
Membrane Entity: Yes 
UniProt
Find proteins for P37299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1U [auth a], GA [auth m]534Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX1OXI3Q0045
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2V [auth b], HA [auth n]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX2OXI1Q0250
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3W [auth c], IA [auth o]269Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX3OXI2Q0275
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialX [auth d], JA [auth p]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX4YGL187CG1362
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 5A, mitochondrialY [auth e], KA [auth q]133Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX5AYNL052WN2474YNL2474W
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialZ [auth f], LA [auth r]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX6YHR051W
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7AA [auth g], MA [auth s]59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX7YMR256CYM9920.10C
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII, mitochondrialBA [auth h], NA [auth t]47Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX8YLR395CL8084.14
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7ACA [auth i], OA [auth u]55Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX9YDL067CD2520
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6BDA [auth j], PA [auth v]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX12YLR038C
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A, mitochondrialEA [auth k], QA [auth w]131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX13YGL191WG1341
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P32799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Cox26FA [auth l], RA [auth x]66Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX26YDR119W-A
Membrane Entity: Yes 
UniProt
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DB [auth E], FB [auth H], GB [auth H], KB [auth L], SB [auth O], VB [auth P], WA [auth C], XB [auth S]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
HEA
Query on HEA

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CC [auth a], DC [auth a], TC [auth m], UC [auth m]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PCF
Query on PCF

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AC [auth T], HD [auth q], IB [auth H], JB [auth I], QB [auth N], QC [auth e], ZA [auth C], ZB [auth S]1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
PEF
Query on PEF

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BB [auth D] , BD [auth n] , CD [auth n] , DD [auth o] , EB [auth E] , ED [auth o] , GC [auth a] , GD [auth q] , 
BB [auth D],  BD [auth n],  CD [auth n],  DD [auth o],  EB [auth E],  ED [auth o],  GC [auth a],  GD [auth q],  HB [auth H],  HC [auth a],  IC [auth a],  ID [auth t],  LC [auth b],  MC [auth c],  NB [auth N],  NC [auth c],  OB [auth N],  PB [auth N],  PC [auth e],  RC [auth h],  SA [auth A],  TB [auth O],  WB [auth P],  XA [auth C],  XC [auth m],  YA [auth C],  YB [auth S],  YC [auth m]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
HEC
Query on HEC

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AB [auth D], RB [auth O]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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LB [auth N], MB [auth N], TA [auth C], UA [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ6
Query on UQ6

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VA [auth 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
FES
Query on FES

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CB [auth E], UB [auth P]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

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AD [auth n], JC [auth b], KC [auth b], ZC [auth n]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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FD [auth p], OC [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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BC [auth a], SC [auth m]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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EC [auth a], VC [auth m]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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FC [auth a], WC [auth m]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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  (Full details and data files)

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