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PDBsum entry 6giq
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protein ligands metals Protein-protein interface(s) links
Electron transport PDB id
6giq

 

 

 

 

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Contents
Protein chains
431 a.a.
352 a.a.
385 a.a.
248 a.a.
185 a.a.
74 a.a.
126 a.a.
93 a.a.
54 a.a.
54 a.a.
44 a.a.
51 a.a.
522 a.a.
235 a.a.
262 a.a.
49 a.a.
96 a.a.
99 a.a.
29 a.a.
31 a.a.
49 a.a.
57 a.a.
18 a.a.
31 a.a.
Ligands
6PH ×2
HEC ×6
8PE ×2
CN5
UQ6 ×2
7PH ×2
FES ×2
PCF ×2
9PE ×2
CN3
HEA
CUA
Metals
_CU
PDB id:
6giq
Name: Electron transport
Title: Saccharomyces cerevisiae respiratory supercomplex iii2iv
Structure: Bj4_g0001550.mRNA.1.Cds.1. Chain: a, l. Synonym: cor1 isoform 1,cytochrome b-c1 complex subunit 1, mitochondrial,y55_g0001550.mRNA.1.Cds.1. Cytochrome b-c1 complex subunit 2, mitochondrial. Chain: b, m. Synonym: qcr2 isoform 1. Cytochrome b. Chain: c, n.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Saccharomyces cerevisiae (strain atcc 204508 / s288c). Organism_taxid: 559292. Strain: atcc 204508 / s288c. Organism_taxid: 4932
Authors: S.Rathore,J.Berndtsson,J.Conrad,M.Ott
Key ref: S.Rathore et al. (2019). Cryo-EM structure of the yeast respiratory supercomplex. Nat Struct Mol Biol, 26, 50-57. PubMed id: 30598556 DOI: 10.1038/s41594-018-0169-7
Date:
15-May-18     Release date:   02-Jan-19    
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.
248 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.
74 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 chain
Pfam   ArchSchema ?
P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		66 a.a.
54 a.a.
Protein chain
Pfam   ArchSchema ?
P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		66 a.a.
54 a.a.
Protein chain
Pfam   ArchSchema ?
P37299  (QCR10_YEAST) -  Cytochrome b-c1 complex subunit 10, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		77 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
P37299  (QCR10_YEAST) -  Cytochrome b-c1 complex subunit 10, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		77 a.a.
51 a.a.
Protein chain
Pfam   ArchSchema ?
P00401  (COX1_YEAST) -  Cytochrome c oxidase subunit 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		534 a.a.
522 a.a.
Protein chain
Pfam   ArchSchema ?
P00410  (COX2_YEAST) -  Cytochrome c oxidase subunit 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		251 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P00420  (COX3_YEAST) -  Cytochrome c oxidase subunit 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		269 a.a.
262 a.a.
Protein chain
Pfam   ArchSchema ?
P04037  (COX4_YEAST) -  Cytochrome c oxidase subunit 4, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
P00424  (COX5A_YEAST) -  Cytochrome c oxidase subunit 5A, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		153 a.a.
96 a.a.
Protein chain
Pfam   ArchSchema ?
P00427  (COX6_YEAST) -  Cytochrome c oxidase subunit 6, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		148 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P10174  (COX7_YEAST) -  Cytochrome c oxidase subunit 7, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		60 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P04039  (COX8_YEAST) -  Cytochrome c oxidase subunit 8, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		78 a.a.
31 a.a.
Protein chain
P07255  (COX9_YEAST) -  Cytochrome c oxidase subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		59 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
Q01519  (COX12_YEAST) -  Cytochrome c oxidase subunit 12, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		83 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
P32799  (COX13_YEAST) -  Cytochrome c oxidase subunit 13, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		129 a.a.
18 a.a.
Protein chain
No UniProt id for this chain
Struc: 31 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class 2: 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)
quinol
 + 2 × Fe(III)-[cytochrome c](out)
 = quinone
 + 2 × Fe(II)- [cytochrome c](out)
 + 2 × H(+)(out)
   Enzyme class 3: Chains a, b, c: 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]
 + 2 × O2
 + 8 × H(+)(in)
 = 4 × Fe(III)-[cytochrome c]
 + 2 × H2O
 + 4 × H(+)(out)
      Cofactor: Cu cation
   Enzyme class 4: Chains d, e, f, g, h, i, j, k: 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: 10.1038/s41594-018-0169-7 Nat Struct Mol Biol 26:50-57 (2019)
PubMed id: 30598556  
 
 
Cryo-EM structure of the yeast respiratory supercomplex.
S.Rathore, J.Berndtsson, L.Marin-Buera, J.Conrad, M.Carroni, P.Brzezinski, M.Ott.
 
  ABSTRACT  
 
Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
 

 

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