2FYN

Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.

Esser, L.Gong, X.Yang, S.Yu, L.Yu, C.A.Xia, D.

(2006) Proc Natl Acad Sci U S A 103: 13045-13050

  • DOI: 10.1073/pnas.0601149103
  • Primary Citation of Related Structures:  
    2FYU, 2FYN

  • PubMed Abstract: 
  • In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site ...

    In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bA, D, G, J, M, P445Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petBfbcB
Membrane Entity: Yes 
UniProt
Find proteins for Q02761 (Rhodobacter sphaeroides)
Explore Q02761 
Go to UniProtKB:  Q02761
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1B, E, H, K, N, Q269Cereibacter sphaeroidesMutation(s): 0 
Gene Names: petCfbcC
Membrane Entity: Yes 
UniProt
Find proteins for Q02760 (Rhodobacter sphaeroides)
Explore Q02760 
Go to UniProtKB:  Q02760
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitC, F, I, L, O, R187Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petAfbcF
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q02762 (Rhodobacter sphaeroides)
Explore Q02762 
Go to UniProtKB:  Q02762
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LOP (Subject of Investigation/LOI)
Query on LOP

Download Ideal Coordinates CCD File 
BA [auth D], HA [auth G], NA [auth J], TA [auth M], V [auth A], ZA [auth P](1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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AB [auth Q] , CA [auth E] , EA [auth G] , FA [auth G] , IA [auth H] , KA [auth J] , LA [auth J] , OA [auth K] , 
AB [auth Q],  CA [auth E],  EA [auth G],  FA [auth G],  IA [auth H],  KA [auth J],  LA [auth J],  OA [auth K],  QA [auth M],  RA [auth M],  S [auth A],  T [auth A],  UA [auth N],  W [auth B],  WA [auth P],  XA [auth P],  Y [auth D],  Z [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA (Subject of Investigation/LOI)
Query on SMA

Download Ideal Coordinates CCD File 
AA [auth D], GA [auth G], MA [auth J], SA [auth M], U [auth A], YA [auth P]STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
BB [auth R], DA [auth F], JA [auth I], PA [auth L], VA [auth O], X [auth C]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.3α = 90
b = 147.13β = 103.94
c = 160.83γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-02-08 
  • Released Date: 2006-08-29 
  • Deposition Author(s): Esser, L., Xia, D.

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance