2QJY

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    2QJP, 2QJK, 2QJY

  • 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 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 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bA, D, G, J, M, P445Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petBfbcB
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, Q269Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: fbcCpetC
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, R187Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petAfbcF
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (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 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download Ideal Coordinates CCD File 
FA [auth D], JB [auth M], QA [auth G], TB [auth P], W [auth A], ZA [auth J](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
Query on HEM

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AA [auth B] , CA [auth D] , DA [auth D] , DB [auth K] , GB [auth M] , HB [auth M] , JA [auth E] , NA [auth G] , 
AA [auth B],  CA [auth D],  DA [auth D],  DB [auth K],  GB [auth M],  HB [auth M],  JA [auth E],  NA [auth G],  NB [auth N],  OA [auth G],  QB [auth P],  RB [auth P],  T [auth A],  TA [auth H],  U [auth A],  WA [auth J],  WB [auth Q],  XA [auth J]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA
Query on SMA

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EA [auth D], IB [auth M], PA [auth G], SB [auth P], V [auth A], YA [auth J]STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
UQ2
Query on UQ2

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AB [auth J], GA [auth D], KB [auth M], RA [auth G], UB [auth P], X [auth A]UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
BGL
Query on BGL

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BB [auth K], HA [auth E], LA [auth G], LB [auth N], PB [auth P], Y [auth B]2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

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BA [auth C], EB [auth L], KA [auth F], OB [auth O], VA [auth I], ZB [auth R]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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CB [auth K] , FB [auth M] , IA [auth E] , MA [auth G] , MB [auth N] , S [auth A] , SA [auth H] , VB [auth Q] , 
CB [auth K],  FB [auth M],  IA [auth E],  MA [auth G],  MB [auth N],  S [auth A],  SA [auth H],  VB [auth Q],  Z [auth B]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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UA [auth I], YB [auth R]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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XB [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SMAKd:  0.699999988079071   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.891α = 90
b = 147.042β = 104.25
c = 161.312γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary