4I7Z

Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.

Hasan, S.S.Stofleth, J.T.Yamashita, E.Cramer, W.A.

(2013) Biochemistry 52: 2649-2654

  • DOI: https://doi.org/10.1021/bi301638h
  • Primary Citation of Related Structures:  
    4I7Z

  • PubMed Abstract: 

    Cytochrome b6f catalyzes quinone redox reactions within photosynthetic membranes to generate a transmembrane proton electrochemical gradient for ATP synthesis. A key step involves the transfer of an electron from the [2Fe-2S] cluster of the iron-sulfur protein (ISP) extrinsic domain to the cytochrome f heme across a distance of 26 Å, which is too large for competent electron transfer but could be bridged by translation-rotation of the ISP. Here we report the first crystallographic evidence of significant motion of the ISP extrinsic domain. It is inferred that extensive crystallographic disorder of the ISP extrinsic domain indicates conformational flexibility. The ISP disorder observed in this structure, in contrast to the largely ordered ISP structure observed in the b6f complex supplemented with neutral lipids, is attributed to electrostatic interactions arising from anionic lipids.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83791 (Mastigocladus laminosus)
Explore P83791 
Go to UniProtKB:  P83791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83791
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4160Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83792 (Mastigocladus laminosus)
Explore P83792 
Go to UniProtKB:  P83792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83792
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f289Mastigocladus laminosusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P83793 (Mastigocladus laminosus)
Explore P83793 
Go to UniProtKB:  P83793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83793
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit179Mastigocladus laminosusMutation(s): 0 
EC: 1.10.9.1
Membrane Entity: Yes 
UniProt
Find proteins for P83794 (Mastigocladus laminosus)
Explore P83794 
Go to UniProtKB:  P83794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83794
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 632Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83795 (Mastigocladus laminosus)
Explore P83795 
Go to UniProtKB:  P83795
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83795
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 735Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83796 (Mastigocladus laminosus)
Explore P83796 
Go to UniProtKB:  P83796
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83796
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 537Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83797 (Mastigocladus laminosus)
Explore P83797 
Go to UniProtKB:  P83797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83797
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 829Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83798 (Mastigocladus laminosus)
Explore P83798 
Go to UniProtKB:  P83798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83798
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
R [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OZ2
Query on OZ2

Download Ideal Coordinates CCD File 
AA [auth G],
T [auth B],
W [auth C]
(2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate
C37 H69 O10 P
YOPHQENQMRACBJ-BMAOJOIDSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
U [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

Download Ideal Coordinates CCD File 
Z [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A]
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
1E2
Query on 1E2

Download Ideal Coordinates CCD File 
X [auth D](2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside
C11 H20 O11 S
GWOURQAWIHLHOD-MPVQUNCYSA-N
8K6
Query on 8K6

Download Ideal Coordinates CCD File 
M [auth A]Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
MYS
Query on MYS

Download Ideal Coordinates CCD File 
L [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
Y [auth F]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
Q [auth A],
S [auth B],
V [auth C]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.451α = 90
b = 159.451β = 90
c = 362.746γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
JBluIce-EPICSdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Non-polymer description