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PDBsum entry 6t0b
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
6t0b

 

 

 

 

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Contents
Protein chains
431 a.a.
352 a.a.
385 a.a.
247 a.a.
185 a.a.
75 a.a.
126 a.a.
93 a.a.
57 a.a.
76 a.a.
534 a.a.
236 a.a.
269 a.a.
120 a.a.
133 a.a.
102 a.a.
59 a.a.
51 a.a.
55 a.a.
75 a.a.
113 a.a.
45 a.a.
99 a.a.
Ligands
CDL ×8
PEF ×26
HEM ×4
PCF ×7
HEC ×2
FES ×2
HEA ×4
CUA ×2
Metals
_ZN ×2
_CU ×2
_CA ×2
_MG ×2
PDB id:
6t0b
Name: Oxidoreductase
Title: The iii2-iv(5b)2 respiratory supercomplex from s. Cerevisiae
Structure: Cytochrome b-c1 complex subunit 1, mitochondrial. Chain: a, l. Synonym: complex iii subunit 1,core protein i,ubiquinol-cytochromE-C reductase complex core protein 1. Cytochrome b-c1 complex subunit 2, mitochondrial. Chain: b, m. Synonym: complex iii subunit 2,core protein ii,ubiquinol-cytochromE-C reductase complex core protein 2. Cytochrome b.
Source: Saccharomyces cerevisiae s288c. Baker's yeast. Organism_taxid: 559292. Gene: cox13, ygl191w, g1341. Expressed in: saccharomyces cerevisiae s288c. Expression_system_taxid: 559292. Expression_system_variant: w303-1b. Organism_taxid: 559292
Authors: A.Marechal,N.Pinotsis,A.Hartley
Key ref: A.M.Hartley et al. (2020). Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Proc Natl Acad Sci U S A, 117, 9329-9337. PubMed id: 32291341 DOI: 10.1073/pnas.1920612117
Date:
02-Oct-19     Release date:   22-Apr-20    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07256  (QCR1_YEAST) -  Cytochrome b-c1 complex subunit 1, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		457 a.a.
431 a.a.
Protein chains
Pfam   ArchSchema ?
P07257  (QCR2_YEAST) -  Cytochrome b-c1 complex subunit 2, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		368 a.a.
352 a.a.
Protein chains
Pfam   ArchSchema ?
P00163  (CYB_YEAST) -  Cytochrome b from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		385 a.a.
385 a.a.
Protein chains
Pfam   ArchSchema ?
P07143  (CY1_YEAST) -  Cytochrome c1, heme protein, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		309 a.a.
247 a.a.
Protein chains
Pfam   ArchSchema ?
P08067  (UCRI_YEAST) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		215 a.a.
185 a.a.
Protein chains
Pfam   ArchSchema ?
P00127  (QCR6_YEAST) -  Cytochrome b-c1 complex subunit 6, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		147 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P00128  (QCR7_YEAST) -  Cytochrome b-c1 complex subunit 7, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		127 a.a.
126 a.a.
Protein chains
Pfam   ArchSchema ?
P08525  (QCR8_YEAST) -  Cytochrome b-c1 complex subunit 8, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		94 a.a.
93 a.a.
Protein chains
Pfam   ArchSchema ?
P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		66 a.a.
57 a.a.
Protein chains
Pfam   ArchSchema ?
P37299  (QCR10_YEAST) -  Cytochrome b-c1 complex subunit 10, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		77 a.a.
76 a.a.
Protein chains
Pfam   ArchSchema ?
P00401  (COX1_YEAST) -  Cytochrome c oxidase subunit 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		534 a.a.
534 a.a.
Protein chains
Pfam   ArchSchema ?
P00410  (COX2_YEAST) -  Cytochrome c oxidase subunit 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		251 a.a.
236 a.a.
Protein chains
Pfam   ArchSchema ?
P00420  (COX3_YEAST) -  Cytochrome c oxidase subunit 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		269 a.a.
269 a.a.
Protein chains
Pfam   ArchSchema ?
P04037  (COX4_YEAST) -  Cytochrome c oxidase subunit 4, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
120 a.a.
Protein chains
Pfam   ArchSchema ?
P00425  (COX5B_YEAST) -  Cytochrome c oxidase subunit 5B, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		151 a.a.
133 a.a.
Protein chains
Pfam   ArchSchema ?
P00427  (COX6_YEAST) -  Cytochrome c oxidase subunit 6, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		148 a.a.
102 a.a.
Protein chains
Pfam   ArchSchema ?
P10174  (COX7_YEAST) -  Cytochrome c oxidase subunit 7, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		60 a.a.
59 a.a.
Protein chains
Pfam   ArchSchema ?
P04039  (COX8_YEAST) -  Cytochrome c oxidase subunit 8, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		78 a.a.
51 a.a.
Protein chains
P07255  (COX9_YEAST) -  Cytochrome c oxidase subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		59 a.a.
55 a.a.
Protein chains
Pfam   ArchSchema ?
Q01519  (COX12_YEAST) -  Cytochrome c oxidase subunit 12, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		83 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P32799  (COX13_YEAST) -  Cytochrome c oxidase subunit 13, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		129 a.a.
113 a.a.
Protein chains
Pfam   ArchSchema ?
Q2V2P9  (COX26_YEAST) -  Cytochrome c oxidase subunit 26, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		66 a.a.
45 a.a.
Protein chains
Pfam   ArchSchema ?
P53721  (RCF2_YEAST) -  Respiratory supercomplex factor 2, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		224 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class 2: Chains a, b, c, n, o, p: E.C.7.1.1.9  - cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 Fe(II)-[cytochrome c] + O2 + 8 H+(in) = 4 Fe(III)-[cytochrome c] + 2 H2O + 4 H+(out)
4 × Fe(II)-[cytochrome c]
 + O2
 + 8 × H(+)(in)
 = 4 × Fe(III)-[cytochrome c]
 + 2 × H2O
 + 4 × H(+)(out)
      Cofactor: Cu cation
   Enzyme class 3: Chains C, D, E, N, O, P: E.C.7.1.1.8  - quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)- [cytochrome c](out) + 2 H(+)(out)
4 × quinol
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity 		+ 2 × Fe(III)-[cytochrome c](out)
 = 8 × quinone
 + 2 × Fe(II)- [cytochrome c](out)
 + 2 × H(+)(out)
   Enzyme class 4: Chains d, e, f, g, h, i, j, k, q, r, s, t, u, v, w, x: E.C.1.9.3.1  - Transferred entry: 7.1.1.9.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
 + 2 × O(2)
 + 4 × H(+)
 = 4 × ferricytochrome c
 + 2 × H(2)O
      Cofactor: Cu cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1073/pnas.1920612117 Proc Natl Acad Sci U S A 117:9329-9337 (2020)
PubMed id: 32291341  
 
 
Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes.
A.M.Hartley, B.Meunier, N.Pinotsis, A.Maréchal.
 
  ABSTRACT  
 
The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In Saccharomyces cerevisiae, cytochrome c oxidase (CIV) forms SCs of varying stoichiometry with cytochrome bc1 (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III2-IV1 and III2-IV2 SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV5B- and CIV5A-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV5B-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC.
 

 

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