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 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83791
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4160Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83792
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f289Mastigocladus laminosusMutation(s): 1 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83793
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit179Mastigocladus laminosusMutation(s): 0 
EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupP83794
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 632Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83795
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 735Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83796
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 537Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83797
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 829Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83798
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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R [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OZ2
Query on OZ2

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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

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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

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Z [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

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

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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

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M [auth A]Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
MYS
Query on MYS

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L [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
OCT
Query on OCT

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Y [auth F]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CD
Query on CD

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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

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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