2PRC

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (UBIQUINONE-2 COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB.

Lancaster, C.R.Michel, H.

(1997) Structure 5: 1339-1359

  • Primary Citation of Related Structures:  
  • Also Cited By: 2JBL, 1DXR

  • PubMed Abstract: 
  • In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In ...

    In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In the original structure of the RC from Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined because in the standard RC crystals it was only approximately 30% occupied with ubiquinone-9 (UQ9). We report here the structural characterization of the QB site by crystallographic refinement of UQ9-depleted RCs and of complexes of the RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor stigmatellin in the QB site.


    Related Citations: 
    • X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1984) J.Mol.Biol. 180: 385
    • Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Deisenhofer, J.,Epp, O.,Sinning, I.,Michel, H.
      (1995) J.Mol.Biol. 246: 429
    • Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1985) Nature 318: 618
    • Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Michel, H.
      (1982) J.Mol.Biol. 158: 567
    • Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications
      Lancaster, C.R.D.
      (1998) Biochim.Biophys.Acta 1365: 143
    • The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
      Deisenhofer, J.,Michel, H.
      (1989) Science 245: 1463
    • Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid
      Lancaster, C.R.D.,Michel, H.
      (1999) J.Mol.Biol. 286: 883


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
C
336Blastochloris viridisGene Names: pufC (cytC)
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
L
273Blastochloris viridisGene Names: pufL
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
M
323Blastochloris viridisGene Names: pufM
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
H
258Blastochloris viridisGene Names: puhA
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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H, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LDA
Query on LDA

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H, L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MQ7
Query on MQ7

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M
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FE2
Query on FE2

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M
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPB
Query on BPB

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L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
UQ2
Query on UQ2

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L
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
BCB
Query on BCB

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L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
NS5
Query on NS5

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M
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
H
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 223.500α = 90.00
b = 223.500β = 90.00
c = 113.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
MOSFLMdata reduction
X-PLORphasing
AGROVATA)data scaling
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model