2WJN | pdb_00002wjn

Lipidic sponge phase crystal structure of photosynthetic reaction centre from Blastochloris viridis (high dose)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.193 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.3 of the entry. See complete history

Literature

Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface.

Wohri, A.B.Wahlgren, W.Y.Malmerberg, E.Johansson, L.C.Neutze, R.Katona, G.

(2009) Biochemistry 48: 9831-9838

  • DOI: https://doi.org/10.1021/bi900545e
  • Primary Citation Related Structures: 
    2WJM, 2WJN

  • PubMed Abstract: 

    Membrane proteins are embedded in a lipid bilayer and maintain strong interactions with lipid molecules. Tightly bound lipids are responsible for vertical positioning and integration of proteins in the membrane and for assembly of multisubunit complexes and occasionally act as substrates. In this work we present the lipidic sponge phase crystal structure of the reaction center from Blastochloris viridis to 1.86 A, which reveals lipid molecules interacting with the protein surface. A diacylglycerol molecule is bound, through a thioether bond, to the N-terminus of the tetraheme cytochrome c subunit. From the electron density recovered at the Q(B) site and the observed change in recombination kinetics in lipidic sponge phase-grown crystals, the mobile ubiquinone appears to be displaced by a monoolein molecule. A 36 A long electron density feature is observed at the interface of transmembrane helices belonging to the H- and M-subunits, probably arising from an unidentified lipid.


  • Organizational Affiliation
    • Department of Chemical and Biological Engineering, Molecular Biotechnology, Chalmers University of Technology, SE-405 30 Gothenburg, Sweden.

Macromolecule Content 

  • Total Structure Weight: 142.87 kDa 
  • Atom Count: 10,590 
  • Modeled Residue Count: 1,171 
  • Deposited Residue Count: 1,192 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNITA [auth C]336Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN H CHAINB [auth H]258Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups
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UniProt GroupP06008
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN L CHAINC [auth L]274Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
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UniProt GroupP06009
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
REACTION CENTER PROTEIN M CHAIND [auth M]324Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups
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UniProt GroupP06010
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB

Query on BCB



Download:Ideal Coordinates CCD File
I [auth L],
J [auth L],
O [auth M],
P [auth M]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB

Query on BPB



Download:Ideal Coordinates CCD File
K [auth L],
Q [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7

Query on MQ7



Download:Ideal Coordinates CCD File
R [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
E [auth C],
F [auth C],
G [auth C],
H [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5

Query on NS5



Download:Ideal Coordinates CCD File
S [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
MPG

Query on MPG



Download:Ideal Coordinates CCD File
L,
M [auth L],
T [auth M]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
N [auth L]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.193 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.76α = 90
b = 139.43β = 90
c = 178.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-12-21
    Changes: Other
  • Version 1.3: 2012-02-01
    Changes: Other
  • Version 2.0: 2017-06-14
    Changes: Advisory, Atomic model, Derived calculations
  • Version 3.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2019-09-25
    Changes: Data collection, Experimental preparation, Other
  • Version 3.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 3.3: 2024-10-16
    Changes: Structure summary