6YMX Electron Transport date Apr 10, 2020
title Ciii2civ Respiratory Supercomplex From Saccharomyces Cerevi
authors J.Berndtsson, S.Rathore, M.Ott
compound source
Molecule: Cytochrome C Oxidase Subunit 1
Chain: a
Synonym: Cytochrome C Oxidase Polypeptide I
Ec: 1.9.3.1
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 2
Chain: b
Synonym: Cytochrome C Oxidase Polypeptide II
Ec: 1.9.3.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 3
Chain: c
Synonym: Cytochrome C Oxidase Polypeptide III
Ec: 1.9.3.1
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 4, Mitochondrial
Chain: d
Synonym: Cytochrome C Oxidase Polypeptide Iv
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 5a, Mitochondrial
Chain: e
Synonym: Cytochrome C Oxidase Polypeptide Va
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 6, Mitochondrial
Chain: f
Synonym: Cytochrome C Oxidase Polypeptide Vi
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 7, Mitochondrial
Chain: g
Synonym: Cytochrome C Oxidase Polypeptide Vii
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 8, Mitochondrial
Chain: h
Synonym: Cytochrome C Oxidase Polypeptide Viii
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 9, Mitochondrial
Chain: I
Synonym: Cytochrome C Oxidase Polypeptide Viia
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 12, Mitochondrial
Chain: j
Synonym: Cytochrome C Oxidase Polypeptide Vib
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 13, Mitochondrial
Chain: k
Synonym: Cytochrome C Oxidase Polypeptide Via
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C Oxidase Subunit 26, Mitochondrial
Chain: m
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 1, Mitochondrial
Chain: A, L
Synonym: Complex III Subunit 1,Core Protein I,Ubiquinol-Cyt Oxidoreductase Core Protein 1,Ubiquinol-Cytochrome C Reduct Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 2, Mitochondrial
Chain: B, M
Synonym: Complex III Subunit 2,Core Protein II,Ubiquinol-Cy Oxidoreductase Core Protein 2;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B
Chain: C, N
Synonym: Complex III Subunit 3,Complex III Subunit Cytb,Com Subunit III,Cytochrome B-C1 Complex Subunit 3,Cytochrome B- Subunit Cytb,Ubiquinol-Cytochrome C Oxidoreductase Complex B Subunit;
Ec: 7.1.1.8
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome C1, Heme Protein, Mitochondrial
Chain: D, O
Synonym: Complex III Subunit 4,Complex III Subunit Iv,Cytoc Complex Subunit 4,Ubiquinol-Cytochrome C Oxidoreductase Cyt Subunit,Cytochrome C-1;
Ec: 7.1.1.8
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit Rieske, Mitochond
Chain: E, P
Synonym: Complex III Subunit 5,Rieske Iron-Sulfur Protein,R Ubiquinol-Cytochrome C Oxidoreductase Iron-Sulfur Subunit;
Ec: 7.1.1.8
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 6, Mitochondrial
Chain: F
Synonym: Complex III Subunit 6,Complex III Subunit Vi,Cytoc Non-Heme 17 Kda Protein,Mitochondrial Hinge Protein,Ubiquin Cytochrome C Oxidoreductase Subunit 6,Ubiquinol-Cytochrome Reductase 17 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 7, Mitochondrial
Chain: G, R
Synonym: Complex III Subunit 7,Complex III Subunit Vii,Ubiq Cytochrome C Oxidoreductase Subunit 7,Ubiquinol-Cytochrome Reductase 14 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 8, Mitochondrial
Chain: H, S
Synonym: Complex III Subunit 8,Complex III Subunit Vii,Ubiq Cytochrome C Oxidoreductase Subunit 8,Ubiquinol-Cytochrome Reductase Complex 11 Kda Protein,Ubiquinone-Binding Protein
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 9, Mitochondrial
Chain: I
Synonym: Complex III Subunit 9,Complex III Subunit X,Cytoch Non-Heme 7.3 Kda Protein,Ubiquinol-Cytochrome C Oxidoreduct Subunit 9,Ubiquinol-Cytochrome C Reductase 7.3 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 6, Mitochondrial
Chain: Q
Synonym: Complex III Subunit 6,Complex III Subunit Vi,Cytoc Non-Heme 17 Kda Protein,Mitochondrial Hinge Protein,Ubiquin Cytochrome C Oxidoreductase Subunit 6,Ubiquinol-Cytochrome Reductase 17 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 9, Mitochondrial
Chain: T
Synonym: Complex III Subunit 9,Complex III Subunit X,Cytoch Non-Heme 7.3 Kda Protein,Ubiquinol-Cytochrome C Oxidoreduct Subunit 9,Ubiquinol-Cytochrome C Reductase 7.3 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 10, Mitochondrial
Chain: U
Synonym: Complex III Subunit 10,Complex III Subunit Xi,Ubiq Cytochrome C Oxidoreductase Subunit 10,Ubiquinol-Cytochrome Reductase 8.5 Kda Protein;
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353

Molecule: Cytochrome B-C1 Complex Subunit 10, Mitochondrial
Chain: V
Synonym: Complex III Subunit 10,Complex III Subunit Xi,Ubiq Cytochrome C Oxidoreductase Subunit 10,Ubiquinol-Cytochrome Reductase 8.5 Kda Protein
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_taxid: 559292
Atcc: 208353
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.17 Å
ligand 6PH, 7PH, 8PE, 9PE, CN3, CN5, CU, CUA, FES, HEA, HEM, PCF, PTY, UQ6, ZN enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, L
  • ubiquinol-cytochrome-c reduc...


    • B, M


    N, C


    R, G


    S, H


    a


    b
  • cytochrome-c oxidase activit...


    • c
  • cytochrome-c oxidase activit...
  • oxidoreduction-driven active...


    • g
  • cytochrome-c oxidase activit...


    • i
  • cytochrome-c oxidase activit...


    • j
  • cytochrome-c oxidase activit...


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (866 Kb) [Save to disk]
  • Biological Unit Coordinates (6ymx.pdb1.gz) 837 Kb
  • LPC: Ligand-Protein Contacts for 6YMX
  • CSU: Contacts of Structural Units for 6YMX
  • Retrieve 6YMX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YMX from S2C, [Save to disk]
    • View 6YMX in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6YMX
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ymx_j] [6ymx_T] [6ymx_d] [6ymx_R] [6ymx_c] [6ymx_A] [6ymx_B] [6ymx_i] [6ymx_f] [6ymx_b] [6ymx_U] [6ymx_Q] [6ymx_H] [6ymx_C] [6ymx_V] [6ymx_a] [6ymx_L] [6ymx_G] [6ymx_M] [6ymx_E] [6ymx_O] [6ymx_P] [6ymx_D] [6ymx_m] [6ymx_h] [6ymx_k] [6ymx_S] [6ymx_N] [6ymx_I] [6ymx_F] [6ymx_e] [6ymx_g]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6YMX
  • Community annotation for 6YMX at PDBWiki (http://pdbwiki.org)

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