6NIN

Rhodobacter sphaeroides bc1 with STIGMATELLIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit.

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

(2019) J Biol Chem 294: 12007-12019

  • DOI: https://doi.org/10.1074/jbc.RA119.008381
  • Primary Citation of Related Structures:  
    6NHG, 6NHH, 6NIN

  • PubMed Abstract: 

    Cytochrome bc 1 complexes (cyt bc 1 ), also known as complex III in mitochondria, are components of the cellular respiratory chain and of the photosynthetic apparatus of non-oxygenic photosynthetic bacteria. They catalyze electron transfer (ET) from ubiquinol to cytochrome c and concomitantly translocate protons across the membrane, contributing to the cross-membrane potential essential for a myriad of cellular activities. This ET-coupled proton translocation reaction requires a gating mechanism that ensures bifurcated electron flow. Here, we report the observation of the Rieske iron-sulfur protein (ISP) in a mobile state, as revealed by the crystal structure of cyt bc 1 from the photosynthetic bacterium Rhodobacter sphaeroides in complex with the fungicide azoxystrobin. Unlike cyt bc 1 inhibitors stigmatellin and famoxadone that immobilize the ISP, azoxystrobin causes the ISP-ED to separate from the cyt b subunit and to remain in a mobile state. Analysis of anomalous scattering signals from the iron-sulfur cluster of the ISP suggests the existence of a trajectory for electron delivery. This work supports and solidifies the hypothesis that the bimodal conformation switch of the ISP provides a gating mechanism for bifurcated ET, which is essential to the Q-cycle mechanism of cyt bc 1 function.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b445Cereibacter sphaeroides 2.4.1Mutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY10 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY10 
Go to UniProtKB:  Q3IY10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY10
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1272Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY11 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY11 
Go to UniProtKB:  Q3IY11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY11
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit187Cereibacter sphaeroides 2.4.1Mutation(s): 1 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY09 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY09 
Go to UniProtKB:  Q3IY09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY09
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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EA [auth F]
HB [auth X]
LA [auth L]
SA [auth P]
W [auth B]
EA [auth F],
HB [auth X],
LA [auth L],
SA [auth P],
W [auth B],
ZA [auth T]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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AA [auth E]
BA [auth E]
DB [auth W]
EB [auth W]
IA [auth K]
AA [auth E],
BA [auth E],
DB [auth W],
EB [auth W],
IA [auth K],
JA [auth K],
PA [auth O],
QA [auth O],
S [auth A],
T [auth A],
WA [auth S],
XA [auth S]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SMA
Query on SMA

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CA [auth E]
FB [auth W]
KA [auth K]
RA [auth O]
U [auth A]
CA [auth E],
FB [auth W],
KA [auth K],
RA [auth O],
U [auth A],
YA [auth S]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
6PE
Query on 6PE

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DA [auth E],
GB [auth W],
V [auth A]
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
BOG
Query on BOG

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BB [auth T]
FA [auth F]
JB [auth X]
NA [auth L]
TA [auth P]
BB [auth T],
FA [auth F],
JB [auth X],
NA [auth L],
TA [auth P],
Y [auth B]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES
Query on FES

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CB [auth U]
HA [auth G]
KB [auth Y]
OA [auth M]
VA [auth Q]
CB [auth U],
HA [auth G],
KB [auth Y],
OA [auth M],
VA [auth Q],
Z [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SR
Query on SR

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AB [auth T]
GA [auth F]
IB [auth X]
MA [auth L]
UA [auth P]
AB [auth T],
GA [auth F],
IB [auth X],
MA [auth L],
UA [auth P],
X [auth B]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 356.661α = 90
b = 145.752β = 104.97
c = 162.223γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary