2WJN

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 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 3.1 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: 10.1021/bi900545e
  • Structures With Same Primary Citation

  • 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 comple ...

    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
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNITC336Blastochloris viridisMutation(s): 0 
Gene Names: pufCcytCBVIRIDIS_00500
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAINH258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAINL274Blastochloris viridisMutation(s): 0 
Gene Names: pufL
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAINM324Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

Download CCD File 
L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
BPB
Query on BPB

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L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
MQ7
Query on MQ7

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

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C
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NS5
Query on NS5

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M
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
MPG
Query on MPG

Download CCD File 
L, M
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
L
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
HL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • 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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Entry History 

Deposition Data

Revision History 

  • 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