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 

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 


View more in-depth experimental data
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