3H1J

Stigmatellin-bound cytochrome bc1 complex from chicken


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Electron Transfer by Domain Movement in Cytochrome Bc1

Zhang, Z.Huang, L.-S.Shulmeister, V.M.Chi, Y.I.Kim, K.K.Hung, L.W.Crofts, A.R.Berry, E.A.Kim, S.-H.

(1998) Nature 392: 677-684

  • DOI: 10.1038/33612
  • Primary Citation of Related Structures:  
    1BCC, 2BCC, 3BCC, 3H1H, 3H1I, 3H1J

  • PubMed Abstract: 
  • The cytochrome bc1 is one of the three major respiratory enzyme complexes residing in the inner mitochondrial membrane. Cytochrome bc1 transfers electrons from ubiquinol to cytochrome c and uses the energy thus released to form an electrochemical gradient across the inner membrane ...

    The cytochrome bc1 is one of the three major respiratory enzyme complexes residing in the inner mitochondrial membrane. Cytochrome bc1 transfers electrons from ubiquinol to cytochrome c and uses the energy thus released to form an electrochemical gradient across the inner membrane. Our X-ray crystal structures of the complex from chicken, cow and rabbit in both the presence and absence of inhibitors of quinone oxidation, reveal two different locations for the extrinsic domain of one component of the enzyme, an iron-sulphur protein. One location is close enough to the supposed quinol oxidation site to allow reduction of the Fe-S protein by ubiquinol. The other site is close enough to cytochrome c1 to allow oxidation of the Fe-S protein by the cytochrome. As neither location will allow both reactions to proceed at a suitable rate, the reaction mechanism must involve movement of the extrinsic domain of the Fe-S component in order to shuttle electrons from ubiquinol to cytochrome c1. Such a mechanism has not previously been observed in redox protein complexes.


    Related Citations: 
    • Structure of the avian mitochondrial cytochrome bc1 complex
      Berry, E.A., Huang, L.-S., Zhang, Z., Kim, S.-H.
      (1999) J Bioenerg Biomembr 31: 177
    • Mitochondrial cytochrome bc1 complex
      Zhang, Z., Berry, E.A., Huang, L.-S., Kim, S.-H.
      (2000) Subcell Biochem 35: 541
    • Physicochemical aspects of the movement of the Rieske iron sulfur protein during quinol oxidation by the bc1 complex from mitochondria and photosynthetic bacteria.
      Crofts, A.R., Hong, S., Zhang, Z., Berry, E.A.
      (1999) Biochemistry 38: 15827

    Organizational Affiliation

    E. O. Lawrence Berkeley National Laboratory, University of California, 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN IA, K [auth N]446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2B, L [auth O]441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC, M [auth P]380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIND, N [auth Q]241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, O [auth R]196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEINF, P [auth S]110Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-CG, Q [auth T]81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIIIH, R [auth U]77Gallus gallusMutation(s): 0 
Gene Names: UQCRHL
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI, S [auth V]47Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEINJ, T [auth W]61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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DB [auth S], GA [auth D], MA [auth G], TA [auth P]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ (Subject of Investigation/LOI)
Query on UQ

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SA [auth P], Y [auth C]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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AA [auth C], BB [auth R], IA [auth E], NA [auth N], UA [auth P], Z [auth C]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
PLC (Subject of Investigation/LOI)
Query on PLC

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CB [auth R], JA [auth E]DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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FA [auth D], YA [auth Q]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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OA [auth P], PA [auth P], V [auth C], W [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA (Subject of Investigation/LOI)
Query on SMA

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RA [auth P], X [auth C]STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
FES
Query on FES

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HA [auth E], ZA [auth R]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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CA [auth C], WA [auth P]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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AB [auth R] , BA [auth C] , DA [auth C] , EA [auth C] , KA [auth E] , LA [auth E] , QA [auth P] , U [auth A] , 
AB [auth R], BA [auth C], DA [auth C], EA [auth C], KA [auth E], LA [auth E], QA [auth P], U [auth A], VA [auth P], XA [auth P]
Unknown ligand
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.464α = 90
b = 182.448β = 90
c = 241.328γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description