3CX5

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.245

Literature

Macromolecules
Sequence Display for 3CX5

Classification: OXIDOREDUCTASE

Total Structure Weight: 534166.88

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome b-c1 complex subunit 1, mitochondrial A, L 431 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Mutation: E153D
Gene Name(s): COR1 QCR1 YBL045C YBL0403
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit 2, mitochondrial B, M 352 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): QCR2 COR2 UCR2 YPR191W P9677.6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B C, N 385 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): COB CYTB Q0105
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c1, heme protein, mitochondrial D, O 248 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): CYT1 CTC1 Gene View YOR065W YOR29-16
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit Rieske, mitochondrial E, P 185 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): RIP1 YEL024W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit 6 F, Q 146 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 2-147
Gene Name(s): QCR6 UCR6 YFR033C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit 7 G, R 126 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 2-127
Gene Name(s): QCR7 CRO1 UCR7 YDR529C D9719.32
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit 8 H, S 93 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): QCR8 YJL166W J0526
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b-c1 complex subunit 9 I, T 65 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 2-66
Gene Name(s): QCR9 UCR9 YGR183C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN (VH) OF FV-FRAGMENT J, U 127 Mus musculus
LIGHT CHAIN (VL) OF FV-FRAGMENT K, V 107 Mus musculus
Cytochrome c iso-1 W 108 Saccharomyces cerevisiae Gene Name(s): CYC1 Gene View YJR048W J1653
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex III (Cytochrome bc1)

Protein Name: Cytochrome bc1


Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CN3
Query on CN3

D, N (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)- 5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]- 4,6,10,12,15-pentaoxa-5,11-diphosphanonadec- 1-yl undecanoate
CARDIOLIPIN (Synonym)
C36 H68 O17 P2
FMNZIMGRZPIVKW-XWHIBYANSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
8PE
Query on 8PE

C, N (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}- 2-(tetradecanoyloxy)propyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE (Synonym)
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CN5
Query on CN5

C (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17- oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec- 1-yl pentadecanoate
CARDIOLIPIN (Synonym)
C26 H52 O13 P2
UKWPDXFRXMWSMQ-VWLOTQADSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C, D, N, O, W PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
9PE
Query on 9PE

C, N (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}- 1-[(heptanoyloxy)methyl]ethyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE (Synonym)
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
6PH
Query on 6PH

A, L (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
PHOSPHATIDIC ACID (Synonym)
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
7PH
Query on 7PH

D, O (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
PHOSPHATIDIC ACID (Synonym)
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SMA
Query on SMA

C, N STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMQ
Query on UMQ

A, L UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE (Synonym)
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

O SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

E, P FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
W L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.245
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 145.12 α = 90.00
b = 165.09 β = 104.09
c = 194.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-04-23
  • Released Date: 2008-05-13
  • Deposition author(s): Solmaz, S.R.N., Hunte, C.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2013-09-25
    Type: Derived calculations