2WJM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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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 of 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.


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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06008
Sequence Annotations
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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)
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Go to UniProtKB:  P06009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Sequence Annotations
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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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06010
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

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J [auth L],
K [auth L],
P [auth M],
Q [auth M]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB
Query on BPB

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L,
R [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7
Query on MQ7

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S [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA
Query on DGA

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I [auth C]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC
Query on HEC

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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

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T [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
MPG
Query on MPG

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M [auth L],
N [auth L],
U [auth M]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
PO4
Query on PO4

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V [auth M],
W [auth M]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE2
Query on FE2

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O [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: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.45α = 90
b = 138.498β = 90
c = 177.77γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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 1.4: 2012-04-25
    Changes: Other
  • Version 2.0: 2017-06-14
    Changes: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 3.0: 2019-01-23
    Changes: 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