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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.jmb.2007.04.011
  • Primary Citation of Related Structures:  
    2E74, 2E75, 2E76

  • 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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83791 (Mastigocladus laminosus)
Explore P83791 
Go to UniProtKB:  P83791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83791
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4160Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83792 (Mastigocladus laminosus)
Explore P83792 
Go to UniProtKB:  P83792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83792
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f289Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83793 (Mastigocladus laminosus)
Explore P83793 
Go to UniProtKB:  P83793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83793
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit179Mastigocladus laminosusMutation(s): 0 
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P83794 (Mastigocladus laminosus)
Explore P83794 
Go to UniProtKB:  P83794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83794
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 632Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83795 (Mastigocladus laminosus)
Explore P83795 
Go to UniProtKB:  P83795
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83795
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 735Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83796 (Mastigocladus laminosus)
Explore P83796 
Go to UniProtKB:  P83796
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83796
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 537Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83797 (Mastigocladus laminosus)
Explore P83797 
Go to UniProtKB:  P83797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83797
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 829Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83798 (Mastigocladus laminosus)
Explore P83798 
Go to UniProtKB:  P83798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83798
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
S [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OPC
Query on OPC

Download Ideal Coordinates CCD File 
M [auth A],
T [auth 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
SQD
Query on SQD

Download Ideal Coordinates CCD File 
X [auth D]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
U [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

Download Ideal Coordinates CCD File 
Y [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A],
V [auth C]
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
QNO
Query on QNO

Download Ideal Coordinates CCD File 
Q [auth A]2-NONYL-4-HYDROXYQUINOLINE N-OXIDE
C18 H25 N O2
LMBFBUICIQJLPK-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
W [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
I [auth A],
R [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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