8C8Q

Cytochrome c oxidase from Schizosaccharomyces pombe


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor.

Moe, A.Adelroth, P.Brzezinski, P.Nasvik Ojemyr, L.

(2023) Commun Chem 6: 32-32

  • DOI: https://doi.org/10.1038/s42004-023-00827-3
  • Primary Citation of Related Structures:  
    8C8Q

  • PubMed Abstract: 

    Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity purified respiratory complex IV (CIV) from S. pombe. The reaction sequence of the reduced enzyme with O 2 proceeds over a time scale of µs-ms, similar to that of the mammalian CIV. The cryo-EM structure of CIV revealed eleven subunits as well as a bound hypoxia-induced gene 1 (Hig1) domain of respiratory supercomplex factor 2 (Rcf2). These results suggest that binding of Rcf2 does not require the presence of a CIII-CIV supercomplex, i.e. Rcf2 is a component of CIV. An AlphaFold-Multimer model suggests that the Hig1 domains of both Rcf1 and Rcf2 bind at the same site of CIV suggesting that their binding is mutually exclusive. Furthermore, the differential functional effect of Rcf1 or Rcf2 is presumably caused by interactions of CIV with their different non-Hig1 domain parts.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1538Schizosaccharomyces pombeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P07657 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP07657
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2248Schizosaccharomyces pombeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P21534 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP21534
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3269Schizosaccharomyces pombeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P14575 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP14575
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrial159Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P79010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP79010
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 5, mitochondrial228Schizosaccharomyces pombeMutation(s): 0 
Gene Names: cox5SPCC338.10c
Membrane Entity: Yes 
UniProt
Find proteins for O74988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO74988
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrial140Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9UTF6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9UTF6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 759Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G2TRP5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupG2TRP5
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII, mitochondrial66Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9P4W1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrial58Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O94705 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrial86Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O94581 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO94581
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrial130Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O74471 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO74471
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory supercomplex factor 2 homolog C1565.01242Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9P3B2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown polypeptide26Schizosaccharomyces pombeMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA (Subject of Investigation/LOI)
Query on HEA

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

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S [auth A],
T [auth B],
V [auth C],
W [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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U [auth B]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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

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P [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

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R [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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Q [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release