1VCR

An icosahedral assembly of light-harvesting chlorophyll a/b protein complex from pea thylakoid membranes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.50 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.379 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes.

Hino, T.Kanamori, E.Shen, J.R.Kouyama, T.

(2004) Acta Crystallogr D Biol Crystallogr 60: 803-809

  • DOI: https://doi.org/10.1107/S0907444904003233
  • Primary Citation of Related Structures:  
    1VCR

  • PubMed Abstract: 

    When the light-harvesting chlorophyll a/b protein complex (LHC-II) from pea thylakoid membranes is co-crystallized with native lipids, an octahedral crystal that exhibits no birefringence is obtained. Cryogenic electron micrographs of a crystal edge showed the crystal to be made up of hollow spherical assemblies with a diameter of 250 A. X-ray diffraction data at 9.5 A resolution revealed the spherical shell of LHC-II to have icosahedral symmetry. A T = 1 icosahedral model of LHC-II, in which the stromal surface of the protein faces outward, was constructed using the previously reported structure of the LHC-II trimer [Kühlbrandt et al. (1994), Nature (London), 367, 614-621]. The present result shows the first example of a well ordered three-dimensional crystal of icosahedral proteoliposomes.


  • Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein AB80232Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07371 (Pisum sativum)
Explore P07371 
Go to UniProtKB:  P07371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07371
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
Query on CHL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.50 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.379 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 360.646α = 90
b = 360.646β = 90
c = 360.646γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-01
    Changes: Data collection, Derived calculations
  • Version 2.0: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2024-04-03
    Changes: Refinement description