1KB9 Oxidoreductase Electron Transport date Nov 05, 2001
title Yeast Cytochrome Bc1 Complex
authors C.Lange, J.H.Nett, B.L.Trumpower, C.Hunte
compound source
Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro
Chain: A
Fragment: Residues 27-457
Ec: 1.10.2.2
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex Core Pro
Chain: B
Fragment: Residues 17-368
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Cytochrome B
Chain: C
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Cytochrome C1, Heme Protein
Chain: D
Fragment: Residues 62-307
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Iron-Sulfur Subu
Chain: E
Fragment: Residues 31-215
Synonym: Rieske Iron-Sulfur Protein, Risp
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 17 Kd Pr
Chain: F
Fragment: Residues 74-147
Synonym: Mitochondrial Hinge Protein, Complex III Polypepti
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 14 Kd Pr
Chain: G
Fragment: Residues 3-127
Synonym: Complex III Subunit Vii
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex Ubiquino Protein Qp-C;
Chain: H
Fragment: Residues 2-94
Synonym: Ubiquinol-Cytochrome C Reductase Complex 11 Kda Pr Complex III Subunit Viii;
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Ubiquinol-Cytochrome C Reductase Complex 7.3 Kd P
Chain: I
Fragment: Residues 4-58
Synonym: Complex III Polypeptide Ix
Ec: 1.10.2.2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Organelle: Mitochondria

Molecule: Heavy Chain (Vh) Of Fv-Fragment
Chain: J
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Light Chain (Vl) Of Fv-Fragment
Chain: K
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask68
symmetry Space Group: C 1 2 1
R_factor 0.218 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
214.473 163.921 147.276 90.00 117.50 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CDL, FES, HEM, PCF, PEF, PIE, SMA, UMQ, UQ6 enzyme Oxidoreductase E.C.1.10.2.2 BRENDA
related structures by homologous chain: 1A0Q, 1BGX, 1EZV, 1I7Z, 1RIE
Gene
Ontology
ChainFunctionProcessComponent
A
  • ubiquinol-cytochrome-c reduc...


    • B


    C


    D


    E


    F


    G


    H


    I


    Primary referenceSpecific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure., Lange C, Nett JH, Trumpower BL, Hunte C, EMBO J 2001 Dec 3;20(23):6591-600. PMID:11726495
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (377 Kb) [Save to disk]
  • Biological Unit Coordinates (1kb9.pdb1.gz) 367 Kb
  • LPC: Ligand-Protein Contacts for 1KB9
  • CSU: Contacts of Structural Units for 1KB9
  • Likely Quarternary Molecular Structure file(s) for 1KB9
  • Retrieve 1KB9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KB9 from S2C, [Save to disk]
    • View 1KB9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1KB9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1KB9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kb9a2, region A:240-457 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9a1, region A:27-239 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9b1, region B:17-218 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9b2, region B:219-368 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9c2, region C:1-261 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9c1, region C:262-385 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9d2, region D:261-307 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9d1, region D:62-260 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9e2, region E:31-86 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9e1, region E:87-215 [Jmol] [rasmolscript] [script source]
        - Domain d1kb9f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1kb9g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1kb9h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1kb9i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1kb9j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1kb9k_, region K [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1kb9] [1kb9_I] [1kb9_K] [1kb9_D] [1kb9_H] [1kb9_C] [1kb9_J] [1kb9_F] [1kb9_E] [1kb9_B] [1kb9_G] [1kb9_A]
  • SWISS-PROT database: [P07143] [P00163] [P07256] [P07257] [P00127] [P00128] [P08525] [P22289] [P08067]
  • Belongs to the proton-translocating quinol:cytochrome c reductase (qcr) superfamily according to TCDB.
  • Domain organization of [CY1_YEAST] [CYB_YEAST] [QCR1_YEAST] [QCR2_YEAST] [QCR6_YEAST] [QCR7_YEAST] [QCR8_YEAST] [QCR9_YEAST] [UCRI_YEAST] by SWISSPFAM
  • Domain found in 1KB9: [IGv ] by SMART
    • Other resources with information on 1KB9
  • Community annotation for 1KB9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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