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 
  • R-Value Observed: 0.215 

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 U S A 110: 4297-4302

  • DOI: 10.1073/pnas.1222248110
  • Structures With Same Primary Citation

  • 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-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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6A215Mastigocladus laminosusMutation(s): 0 
Gene Names: petB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83791 (Mastigocladus laminosus)
Explore P83791 
Go to UniProtKB:  P83791
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 4B160Mastigocladus laminosusMutation(s): 0 
Gene Names: petD
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83792 (Mastigocladus laminosus)
Explore P83792 
Go to UniProtKB:  P83792
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome fC289Mastigocladus laminosusMutation(s): 0 
Gene Names: petA
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83793 (Mastigocladus laminosus)
Explore P83793 
Go to UniProtKB:  P83793
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex iron-sulfur subunitD179Mastigocladus laminosusMutation(s): 0 
Gene Names: petC
EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83794 (Mastigocladus laminosus)
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 6E32Mastigocladus laminosusMutation(s): 0 
Gene Names: petL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83795 (Mastigocladus laminosus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 7F35Mastigocladus laminosusMutation(s): 0 
Gene Names: petM
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83796 (Mastigocladus laminosus)
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  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 8H29Mastigocladus laminosusMutation(s): 0 
Gene Names: petN
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83798 (Mastigocladus laminosus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 5G37Mastigocladus laminosusMutation(s): 0 
Gene Names: petG
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex with bound TDS:
Find proteins for P83797 (Mastigocladus laminosus)
Explore P83797 
Go to UniProtKB:  P83797
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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B
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 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
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
 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
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
HEM
Query on HEM

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A, C
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
7PH
Query on 7PH

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

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

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A, B
UNDECYL-MALTOSIDE
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
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
 Ligand Interaction
8K6
Query on 8K6

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

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

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D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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F
N-OCTANE
C8 H18
TVMXDCGIABBOFY-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 
  • R-Value Observed: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.197α = 90
b = 157.197β = 90
c = 363.276γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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