6NHH

Rhodobacter sphaeroides bc1 with azoxystrobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1074/jbc.RA119.008381
  • Primary Citation of Related Structures:  
    6NHH, 6NHG, 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 ...

    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

    Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892 xiad@mail.nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bA, D [auth E]445Rhodobacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: fbcBRSP_1395
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY10 (Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY10 
Go to UniProtKB:  Q3IY10
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1B, E [auth F]272Rhodobacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: fbcCRSP_1394
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY11 (Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY11 
Go to UniProtKB:  Q3IY11
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitC, F [auth G]187Rhodobacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: fbcFRSP_1396
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY09 (Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY09 
Go to UniProtKB:  Q3IY09
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
N [auth B], V [auth F]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], Q [auth E], R [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
8SP
Query on 8SP

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K [auth A], W [auth F]O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C22 H42 N O10 P
TWOCGGYLNFTSJO-MOPGFXCFSA-N
 Ligand Interaction
6PE
Query on 6PE

Download Ideal Coordinates CCD File 
J [auth A], T [auth E]1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
 Ligand Interaction
AZO
Query on AZO

Download Ideal Coordinates CCD File 
I [auth A], S [auth E]METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE
C22 H17 N3 O5
WFDXOXNFNRHQEC-GHRIWEEISA-N
 Ligand Interaction
BOG
Query on BOG

Download Ideal Coordinates CCD File 
M [auth B], U [auth F]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
P [auth C], Y [auth G]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download Ideal Coordinates CCD File 
L [auth A], O [auth B], X [auth F]STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.309α = 90
b = 154.655β = 95.36
c = 100.939γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



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