8Q1B | pdb_00008q1b

III2-IV1 respiratory supercomplex from S. pombe


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history

Literature

Structure and function of the S. pombe III-IV-cyt c supercomplex.

Moe, A.Dimogkioka, A.R.Rapaport, D.Ojemyr, L.N.Brzezinski, P.

(2023) Proc Natl Acad Sci U S A 120: e2307697120-e2307697120

  • DOI: https://doi.org/10.1073/pnas.2307697120
  • Primary Citation Related Structures: 
    8Q1B

  • PubMed Abstract: 

    The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII 2 ), via a mobile electron carrier, cytochrome c . In the present study, we isolated the CIII 2 CIV supercomplex from the fission yeast Schizosaccharomyces pombe and determined its structure with bound cyt. c using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn 2+ , coordinated in the CIII subunit Cor1, which is encoded by the same gene ( qcr 1 ) as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIII 2 CIV supercomplex displays proteolytic activity suggesting a dual role of CIII 2 in S. pombe . As in the supercomplex from S. cerevisiae , subunit Cox5 of CIV faces towards one CIII monomer, but in S. pombe, the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. c binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. c bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII 2 respiratory system and indicates a two-dimensional cyt. c diffusion mechanism within the CIII 2 -CIV supercomplex.


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

Macromolecule Content 

  • Total Structure Weight: 813.49 kDa 
  • Atom Count: 48,686 
  • Modeled Residue Count: 5,974 
  • Deposited Residue Count: 7,037 
  • Unique protein chains: 23

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit betaA,
K [auth L]
457Schizosaccharomyces pombeMutation(s): 0 
EC: 3.4.24.64
Membrane Entity: Yes 
UniProt
Find proteins for Q9P7X1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9P7X1
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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]
426Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P78761 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bC,
M [auth N]
387Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05501 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
N [auth O]
307Schizosaccharomyces pombeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for O59680 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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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]
228Schizosaccharomyces pombeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q09154 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F,
P [auth Q]
214Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O42932 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7G,
Q [auth R]
137Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O74533 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8H,
R [auth S]
92Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50523 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I,
S [auth T]
67Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O74433 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10J,
T [auth U]
79Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9P7E0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1U [auth a]538Schizosaccharomyces 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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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2V [auth b]248Schizosaccharomyces 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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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3W [auth c]269Schizosaccharomyces 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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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialX [auth d]159Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P79010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 5, mitochondrialY [auth e]228Schizosaccharomyces 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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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialZ [auth f]140Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9UTF6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7AA [auth g]59Schizosaccharomyces 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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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII, mitochondrialBA [auth h]66Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9P4W1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialCA [auth i]58Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O94705 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrialDA [auth j]86Schizosaccharomyces 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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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialEA [auth k]130Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O74471 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Respiratory supercomplex factor 2 homolog C1565.01FA [auth l]242Schizosaccharomyces pombeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9P3B2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown polypeptideGA [auth m]26Schizosaccharomyces pombeMutation(s): 0 

Small Molecules

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

Query on CDL



Download:Ideal Coordinates CCD File
GB [auth S]
HB [auth S]
IA [auth A]
SA [auth H]
TA [auth H]
GB [auth S],
HB [auth S],
IA [auth A],
SA [auth H],
TA [auth H],
WA [auth L]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10

Query on U10



Download:Ideal Coordinates CCD File
AB [auth N],
OA [auth C]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
HEA

Query on HEA



Download:Ideal Coordinates CCD File
JB [auth a],
KB [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PCF

Query on PCF



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IB [auth T],
JA [auth A],
LA [auth A],
XA [auth L]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
PEF

Query on PEF



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BB [auth N]
CB [auth N]
EB [auth O]
KA [auth A]
NB [auth a]
BB [auth N],
CB [auth N],
EB [auth O],
KA [auth A],
NB [auth a],
PB [auth b],
QA [auth D],
RB [auth c],
TB [auth k],
UA [auth J]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEC

Query on HEC



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

Query on HEM



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MA [auth C],
NA [auth C],
YA [auth N],
ZA [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES

Query on FES



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

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QB [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN



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HA [auth A],
SB [auth d],
VA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



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LB [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA

Query on CA



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MB [auth a]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



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OB [auth b]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2023-11-15
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.3: 2025-12-17
    Changes: Data collection