4H13

Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex

Hasan, S.S.Yamashita, E.Baniulis, D.Cramer, W.A.

(2013) Proc.Natl.Acad.Sci.USA 110: 4297-4302

  • DOI: 10.1073/pnas.1222248110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygenic photosynthesis is generated by the cytochrome b6f complex. The proton uptake pathway from the electrochemically negative (n) aqueous phase to the n-si ...

    As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygenic photosynthesis is generated by the cytochrome b6f complex. The proton uptake pathway from the electrochemically negative (n) aqueous phase to the n-side quinone binding site of the complex, and a probable route for proton exit to the positive phase resulting from quinol oxidation, are defined in a 2.70-Å crystal structure and in structures with quinone analog inhibitors at 3.07 Å (tridecyl-stigmatellin) and 3.25-Å (2-nonyl-4-hydroxyquinoline N-oxide) resolution. The simplest n-side proton pathway extends from the aqueous phase via Asp20 and Arg207 (cytochrome b6 subunit) to quinone bound axially to heme c(n). On the positive side, the heme-proximal Glu78 (subunit IV), which accepts protons from plastosemiquinone, defines a route for H(+) transfer to the aqueous phase. These pathways provide a structure-based description of the quinone-mediated proton transfer responsible for generation of the transmembrane electrochemical potential gradient in oxygenic photosynthesis.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6
A
215Mastigocladus laminosusMutation(s): 0 
Gene Names: petB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83792 (Mastigocladus laminosus)
Go to UniProtKB:  P83792
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome f
C
289Mastigocladus laminosusMutation(s): 0 
Gene Names: petA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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: 1.10.9.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83798 (Mastigocladus laminosus)
Go to UniProtKB:  P83798
Small Molecules
Ligands 13 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
SQD
Query on SQD

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D
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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B
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
7PH
Query on 7PH

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C
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
PHOSPHATIDIC ACID
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
 Ligand Interaction
OPC
Query on OPC

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A, B
(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
DIOLEOYL-PHOSPHATIDYLCHOLINE
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
 Ligand Interaction
FES
Query on FES

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D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 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, B
UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
TDS
Query on TDS

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A, B
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
TRIDECYL-STIGMATELLIN
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-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
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
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.214 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 157.197α = 90.00
b = 157.197β = 90.00
c = 363.276γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references