4I7Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/bi301638h

  • 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-sulf ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6
A
215Mastigocladus laminosusMutation(s): 0 
Gene Names: petB
Find proteins for P83791 (Mastigocladus laminosus)
Go to UniProtKB:  P83791
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 4
B
160Mastigocladus laminosusMutation(s): 0 
Gene Names: petD
Find proteins for P83792 (Mastigocladus laminosus)
Go to UniProtKB:  P83792
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome f
C
289Mastigocladus laminosusMutation(s): 1 
Gene Names: petA
Find proteins for P83793 (Mastigocladus laminosus)
Go to UniProtKB:  P83793
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex iron-sulfur subunit
D
179Mastigocladus laminosusMutation(s): 0 
Gene Names: petC
EC: 7.1.1.6
Find proteins for P83794 (Mastigocladus laminosus)
Go to UniProtKB:  P83794
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 6
E
32Mastigocladus laminosusMutation(s): 0 
Gene Names: petL
Find proteins for P83795 (Mastigocladus laminosus)
Go to UniProtKB:  P83795
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 7
F
35Mastigocladus laminosusMutation(s): 0 
Gene Names: petM
Find proteins for P83796 (Mastigocladus laminosus)
Go to UniProtKB:  P83796
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 5
G
37Mastigocladus laminosusMutation(s): 0 
Gene Names: petG
Find proteins for P83797 (Mastigocladus laminosus)
Go to UniProtKB:  P83797
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 8
H
29Mastigocladus laminosusMutation(s): 0 
Gene Names: petN
Find proteins for P83798 (Mastigocladus laminosus)
Go to UniProtKB:  P83798
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

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F
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
OZ2
Query on OZ2

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B, C, G
(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
 Ligand Interaction
CLA
Query on CLA

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B
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
8K6
Query on 8K6

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A
Octadecane
N-Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
 Ligand Interaction
UMQ
Query on UMQ

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A
UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
HEM
Query on HEM

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A, C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
1E2
Query on 1E2

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D
(2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside
C11 H20 O11 S
GWOURQAWIHLHOD-MPVQUNCYSA-N
 Ligand Interaction
BCR
Query on BCR

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G
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
MYS
Query on MYS

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A
PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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A, B, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 159.451α = 90.00
b = 159.451β = 90.00
c = 362.746γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
JBluIce-EPICSdata collection
REFMACphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-12-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description