2QJK

Crystal Structure Analysis of mutant rhodobacter sphaeroides bc1 with stigmatellin and antimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    2QJK, 2QJP, 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 b
A, D, G, J, M, P
A, D, G, J, M, P
428Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petBfbcB
Membrane Entity: Yes 
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides)
Explore Q02761 
Go to UniProtKB:  Q02761
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02761
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1
B, E, H, K, N, Q
B, E, H, K, N, Q
256Cereibacter sphaeroidesMutation(s): 0 
Gene Names: fbcCpetC
Membrane Entity: Yes 
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides)
Explore Q02760 
Go to UniProtKB:  Q02760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02760
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, F, I, L, O, R
C, F, I, L, O, R
179Cereibacter 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 (Cereibacter sphaeroides)
Explore Q02762 
Go to UniProtKB:  Q02762
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02762
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download Ideal Coordinates CCD File 
FA [auth D],
GB [auth M],
OA [auth G],
OB [auth P],
W [auth A],
FA [auth D],
GB [auth M],
OA [auth G],
OB [auth P],
W [auth A],
XA [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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AB [auth K],
CA [auth D],
DA [auth D],
DB [auth M],
EB [auth M],
AB [auth K],
CA [auth D],
DA [auth D],
DB [auth M],
EB [auth M],
IA [auth E],
JB [auth N],
LA [auth G],
LB [auth P],
MA [auth G],
MB [auth P],
RA [auth H],
SB [auth Q],
T [auth A],
U [auth A],
UA [auth J],
VA [auth J],
Z [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ANJ
Query on ANJ

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GA [auth D],
HB [auth M],
PA [auth G],
PB [auth P],
X [auth A],
GA [auth D],
HB [auth M],
PA [auth G],
PB [auth P],
X [auth A],
YA [auth J]
(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE
C28 H40 N2 O9
UPHOMQADKXDOFD-UKHQZXFMSA-N
 Ligand Interaction
SMA
Query on SMA

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EA [auth D],
FB [auth M],
NA [auth G],
NB [auth P],
V [auth A],
EA [auth D],
FB [auth M],
NA [auth G],
NB [auth P],
V [auth A],
WA [auth J]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
BGL
Query on BGL

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BA [auth D],
CB [auth M],
KA [auth G],
QB [auth Q],
S [auth A],
BA [auth D],
CB [auth M],
KA [auth G],
QB [auth Q],
S [auth A],
TA [auth J]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

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AA [auth C],
BB [auth L],
JA [auth F],
KB [auth O],
SA [auth I],
AA [auth C],
BB [auth L],
JA [auth F],
KB [auth O],
SA [auth I],
TB [auth R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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HA [auth E],
IB [auth N],
QA [auth H],
RB [auth Q],
Y [auth B],
HA [auth E],
IB [auth N],
QA [auth H],
RB [auth Q],
Y [auth B],
ZA [auth K]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 352.291α = 90
b = 147.396β = 104.13
c = 160.762γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-12-25 
  • Deposition Author(s): Esser, L.

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Structure summary