2QJY

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.

Esser, L.Elberry, M.Zhou, F.Yu, C.A.Yu, L.Xia, D.

(2008) J.Biol.Chem. 283: 2846-2857

  • DOI: 10.1074/jbc.M708608200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cytochrome bc(1) complex (bc(1)) is a major contributor to the proton motive force across the membrane by coupling electron transfer to proton translocation. The crystal structures of wild type and mutant bc(1) complexes from the photosynthetic p ...

    The cytochrome bc(1) complex (bc(1)) is a major contributor to the proton motive force across the membrane by coupling electron transfer to proton translocation. The crystal structures of wild type and mutant bc(1) complexes from the photosynthetic purple bacterium Rhodobacter sphaeroides (Rsbc(1)), stabilized with the quinol oxidation (Q(P)) site inhibitor stigmatellin alone or in combination with the quinone reduction (Q(N)) site inhibitor antimycin, were determined. The high quality electron density permitted assignments of a new metal-binding site to the cytochrome c(1) subunit and a number of lipid and detergent molecules. Structural differences between Rsbc(1) and its mitochondrial counterparts are mostly extra membranous and provide a basis for understanding the function of the predominantly longer sequences in the bacterial subunits. Functional implications for the bc(1) complex are derived from analyses of 10 independent molecules in various crystal forms and from comparisons with mitochondrial complexes.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
A, D, G, J, M, P
445Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petB (fbcB)
Find proteins for Q02761 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1
B, E, H, K, N, Q
269Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: petC (fbcC)
Find proteins for Q02760 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, F, I, L, O, R
187Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petA (fbcF)
EC: 7.1.1.8
Find proteins for Q02762 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02762
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGL
Query on BGL

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Download CCD File 
B, E, G, K, N, P
B-2-OCTYLGLUCOSIDE
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
NA
Query on NA

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R
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LOP
Query on LOP

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Download CCD File 
A, D, G, J, M, P
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
 Ligand Interaction
CL
Query on CL

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I, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FES
Query on FES

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C, F, I, L, O, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A, B, D, E, G, H, J, K, M, N, P, Q
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA
Query on SMA

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A, D, G, J, M, P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
UQ2
Query on UQ2

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Download CCD File 
A, D, G, J, M, P
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
SR
Query on SR

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Download CCD File 
A, B, E, G, H, K, M, N, Q
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SMAKd: ~0.7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 351.891α = 90.00
b = 147.042β = 104.25
c = 161.312γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-07-09 
  • Released Date: 2007-12-25 
  • Deposition Author(s): Esser, L., Xia, D.

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance