spacer
spacer

PDBsum entry 6hu9
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase/electron transport PDB id
6hu9

 

 

 

 

Loading ...

 
JSmol PyMol  
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.
121 a.a.
133 a.a.
102 a.a.
59 a.a.
47 a.a.
55 a.a.
77 a.a.
113 a.a.
45 a.a.
Ligands
PEF ×28
HEM ×4
UQ6
CDL ×8
PCF ×8
HEC ×2
FES ×2
HEA ×4
Metals
_ZN ×2
_CU ×2
_CA ×2
_MG ×2
CUA ×4
PDB id:
6hu9
Name: Oxidoreductase/electron transport
Title: Iii2-iv2 mitochondrial 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 (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: cox13, ygl191w, g1341. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Strain: atcc 204508 / s288c
Authors: A.M.Hartley,N.Pinotsis,A.Marechal
Key ref: A.M.Hartley et al. (2019). Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1. Nat Struct Mol Biol, 26, 78-83. PubMed id: 30598554 DOI: 10.1038/s41594-018-0172-z
Date:
05-Oct-18     Release date:   26-Dec-18    
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.
121 a.a.
Protein chains
Pfam   ArchSchema ?
P00424  (COX5A_YEAST) -  Cytochrome c oxidase subunit 5A, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		153 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.
47 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.
77 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.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class 2: Chains a, b, c, m, n, o: 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
 + 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, p, q, r, s, t, u, v, w: 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/s41594-018-0172-z Nat Struct Mol Biol 26:78-83 (2019)
PubMed id: 30598554  
 
 
Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.
A.M.Hartley, N.Lukoyanova, Y.Zhang, A.Cabrera-Orefice, S.Arnold, B.Meunier, N.Pinotsis, A.Maréchal.
 
  ABSTRACT  
 
Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III2IV2 SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.
 

 

spacer
spacer