7Z10

Monomeric respiratory complex IV isolated from S. cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structure of a monomeric yeast S. cerevisiae complex IV isolated with maltosides: Implications in supercomplex formation.

Ing, G.Hartley, A.M.Pinotsis, N.Marechal, A.

(2022) Biochim Biophys Acta Bioenerg 1863: 148591-148591

  • DOI: https://doi.org/10.1016/j.bbabio.2022.148591
  • Primary Citation of Related Structures:  
    7Z10

  • PubMed Abstract: 

    In mitochondria, complex IV (CIV) can be found as a monomer, a dimer or in association with other respiratory complexes. The atomic structure of the yeast S. cerevisiae CIV in a supercomplex (SC) with complex III (CIII) pointed to a region of significant conformational changes compared to the homologous mammalian CIV structures. These changes involved the matrix side domain of Cox5A at the CIII-CIV interface, and it was suggested that it could be required for SC formation. To investigate this, we solved the structure of the isolated monomeric CIV from S. cerevisiae stabilised in amphipol A8-35 at 3.9 Å using cryo-electron microscopy. Only a minor change in flexibility was seen in this Cox5A region, ruling out large CIV conformational shift for interaction with CIII and confirming the different fold of the yeast Cox5A subunit compared to mammalian homologues. Other differences in structure were the absence of two canonical subunits, Cox12 and Cox13, as well as Cox26, which is unique to the yeast CIV. Their absence is most likely due to the protein purification protocol used to isolate CIV from the III-IV SC.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A [auth a]534Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00401
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth b]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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UniProt GroupP00410
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3C [auth c]269Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00420
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialD [auth d]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX4YGL187CG1362
Membrane Entity: Yes 
UniProt
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP04037
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 5A, mitochondrialE [auth e]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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialF [auth f]104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX6YHR051W
Membrane Entity: Yes 
UniProt
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7G [auth g]59Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP10174
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII, mitochondrialH [auth h]47Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX8YLR395CL8084.14
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P04039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9I [auth i]55Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07255
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA (Subject of Investigation/LOI)
Query on HEA

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K [auth a],
L [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEF (Subject of Investigation/LOI)
Query on PEF

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N [auth a],
O [auth a],
Q [auth c]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
CUA (Subject of Investigation/LOI)
Query on CUA

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P [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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R [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

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J [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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M [auth a]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M00936X/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references, Derived calculations