2DRE

Crystal structure of Water-soluble chlorophyll protein from lepidium virginicum at 2.00 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein.

Horigome, D.Satoh, H.Itoh, N.Mitsunaga, K.Oonishi, I.Nakagawa, A.Uchida, A.

(2007) J Biol Chem 282: 6525-6531

  • DOI: 10.1074/jbc.M609458200
  • Primary Citation of Related Structures:  
    2DRE

  • PubMed Abstract: 
  • A water-soluble chlorophyll-binding protein (WSCP) is the single known instance of a putative chlorophyll (Chl) carrier in green plants. Recently the photoprotective function of WSCP has been demonstrated by EPR measurements; the light-induced singlet-oxygen formation of Chl in the WSCP tetramer is about four times lower than that of unbound Chl ...

    A water-soluble chlorophyll-binding protein (WSCP) is the single known instance of a putative chlorophyll (Chl) carrier in green plants. Recently the photoprotective function of WSCP has been demonstrated by EPR measurements; the light-induced singlet-oxygen formation of Chl in the WSCP tetramer is about four times lower than that of unbound Chl. This paper describes the crystal structure of the WSCP-Chl complex purified from leaves of Lepidium virginicum (Virginia pepperweed) to clarify the mechanism of its photoprotective function. The WSCP-Chl complex is a homotetramer comprising four protein chains of 180 amino acids and four Chl molecules. At the center of the complex one hydrophobic cavity is formed in which all of the four Chl molecules are tightly packed and isolated from bulk solvent. With reference to the novel Chl-binding mode, we propose that the photoprotection mechanism may be based on the inhibition of physical contact between the Chl molecules and molecular oxygen.


    Related Citations: 
    • Water-soluble chlorophyll protein in Brassicaceae plants is a stress-induced chlorophyll-binding protein
      Satoh, H., Uchida, A., Nakayama, K., Okada, M.
      (2001) Plant Cell Physiol 42: 906
    • Crystallization of water-soluble chlorophyll-proteins from Lepidium virginicum
      Murata, T., Itoh, R., Yakushiji, E.
      (1980) Biochim Biophys Acta 593: 167

    Organizational Affiliation

    Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Water-soluble chlorophyll proteinA, B, C, D180Lepidium virginicumMutation(s): 0 
Gene Names: WSCP1
UniProt
Find proteins for O04797 (Lepidium virginicum)
Explore O04797 
Go to UniProtKB:  O04797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO04797
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.06α = 90
b = 82.73β = 90
c = 121.88γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance