2E75

Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide (NQNO) from M.laminosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n)

Yamashita, E.Zhang, H.Cramer, W.A.

(2007) J Mol Biol 370: 39-52

  • DOI: 10.1016/j.jmb.2007.04.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A native structure of the cytochrome b(6)f complex with improved resolution was obtained from crystals of the complex grown in the presence of divalent cadmium. Two Cd(2+) binding sites with different occupancy were determined: (i) a higher affinity ...

    A native structure of the cytochrome b(6)f complex with improved resolution was obtained from crystals of the complex grown in the presence of divalent cadmium. Two Cd(2+) binding sites with different occupancy were determined: (i) a higher affinity site, Cd1, which bridges His143 of cytochrome f and the acidic residue, Glu75, of cyt b(6); in addition, Cd1 is coordinated by 1-2 H(2)O or 1-2 Cl(-); (ii) a second site, Cd2, of lower affinity for which three identified ligands are Asp58 (subunit IV), Glu3 (PetG subunit) and Glu4 (PetM subunit). Binding sites of quinone analogue inhibitors were sought to map the pathway of transfer of the lipophilic quinone across the b(6)f complex and to define the function of the novel heme c(n). Two sites were found for the chromone ring of the tridecyl-stigmatellin (TDS) quinone analogue inhibitor, one near the p-side [2Fe-2S] cluster. A second TDS site was found on the n-side of the complex facing the quinone exchange cavity as an axial ligand of heme c(n). A similar binding site proximal to heme c(n) was found for the n-side inhibitor, NQNO. Binding of these inhibitors required their addition to the complex before lipid used to facilitate crystallization. The similar binding of NQNO and TDS as axial ligands to heme c(n) implies that this heme utilizes plastoquinone as a natural ligand, thus defining an electron transfer complex consisting of hemes b(n), c(n), and PQ, and the pathway of n-side reduction of the PQ pool. The NQNO binding site explains several effects associated with its inhibitory action: the negative shift in heme c(n) midpoint potential, the increased amplitude of light-induced heme b(n) reduction, and an altered EPR spectrum attributed to interaction between hemes c(n) and b(n). A decreased extent of heme c(n) reduction by reduced ferredoxin in the presence of NQNO allows observation of the heme c(n) Soret band in a chemical difference spectrum.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State St., West Lafayette, IN 47907, USA.



Macromolecules

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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, native structure
Find proteins for P83792 (Mastigocladus laminosus)
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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: 1.10.99.1 (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, native structure
Find proteins for P83794 (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, native structure
Find proteins for P83798 (Mastigocladus laminosus)
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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, native structure
Find proteins for P83791 (Mastigocladus laminosus)
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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, native structure
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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, native structure
Find proteins for P83795 (Mastigocladus laminosus)
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  • Reference Sequence

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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, native structure
Find proteins for P83796 (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, native structure
Find proteins for P83797 (Mastigocladus laminosus)
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  • Reference Sequence
Small Molecules
Ligands 9 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
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, C
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
QNO
Query on QNO

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A
2-NONYL-4-HYDROXYQUINOLINE N-OXIDE
C18 H25 N O2
LMBFBUICIQJLPK-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.164α = 90
b = 159.164β = 90
c = 362.269γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Version format compliance