3O18

Crystal structure of c-phycocyanin from Themosynechococcus vulcanus at 1.35 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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This is version 1.1 of the entry. See complete history


Literature

High-resolution crystal structures of trimeric and rod phycocyanin.

David, L.Marx, A.Adir, N.

(2011) J Mol Biol 405: 201-213

  • DOI: 10.1016/j.jmb.2010.10.036
  • Primary Citation of Related Structures:  
    3O18, 3O2C

  • PubMed Abstract: 
  • The phycobilisome light-harvesting antenna in cyanobacteria and red algae is assembled from two substructures: a central core composed of allophycocyanin surrounded by rods that always contain phycocyanin (PC). Unpigmented proteins called linkers are also found within the rods and core ...

    The phycobilisome light-harvesting antenna in cyanobacteria and red algae is assembled from two substructures: a central core composed of allophycocyanin surrounded by rods that always contain phycocyanin (PC). Unpigmented proteins called linkers are also found within the rods and core. We present here two new structures of PC from the thermophilic cyanobacterium Thermosynechococcus vulcanus. We have determined the structure of trimeric PC to 1.35 Å, the highest resolution reported to date for this protein. We also present a structure of PC isolated in its intact and functional rod form at 1.5 Å. Analysis of rod crystals showed that in addition to the α and β PC subunit, there were three linker proteins: the capping rod linker (L(R)(8.7)), the rod linker (L(R)), and only one of three rod-core linkers (L(RC), CpcG4) with a stoichiometry of 12:12:1:1:1. This ratio indicates that the crystals contained rods composed of two hexamers. The crystallographic parameters of the rod crystals are nearly identical with that of the trimeric form, indicating that the linkers do not affect crystal packing and are completely embedded within the rod cavities. Absorption and fluorescence emission spectra were red-shifted, as expected for assembled rods, and this could be shown for the rod in solution as well as in crystal using confocal fluorescence microscopy. The crystal packing imparts superimposition of the three rod linkers, canceling out their electron density. However, analysis of B-factors and the conformations of residues facing the rod channel indicate the presence of linkers. Based on the experimental evidence presented here and a homology-based model of the L(R) protein, we suggest that the linkers do not in fact link between rod hexamers but stabilize the hexameric assembly and modify rod energy absorption and transfer capabilities.


    Organizational Affiliation

    Schulich Faculty of Chemistry, Israel Institute of Technology, Haifa, 32000 Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin alpha subunitA162Thermosynechococcus vulcanusMutation(s): 0 
UniProt
Find proteins for Q9AM02 (Thermosynechococcus vulcanus)
Explore Q9AM02 
Go to UniProtKB:  Q9AM02
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin beta subunitB172Thermosynechococcus vulcanusMutation(s): 0 
UniProt
Find proteins for Q71RW8 (Thermosynechococcus vulcanus)
Explore Q71RW8 
Go to UniProtKB:  Q71RW8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
C [auth A], D [auth B], E [auth B]PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
BL-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.807α = 90
b = 186.807β = 90
c = 59.822γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance