1QGW

CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYTE RHODOMONAS CS24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution.

Wilk, K.E.Harrop, S.J.Jankova, L.Edler, D.Keenan, G.Sharples, F.Hiller, R.G.Curmi, P.M.

(1999) Proc Natl Acad Sci U S A 96: 8901-8906

  • DOI: 10.1073/pnas.96.16.8901
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble ...

    Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels. The crystal structure of the heterodimeric alpha(1)alpha(2)betabeta PE 545 from the marine cryptophyte Rhodomonas CS24 has been determined at 1.63-A resolution. Although the beta-chain structure is similar to the alpha and beta chains of other known phycobiliproteins, the overall structure of PE 545 is novel with the alpha chains forming a simple extended fold with an antiparallel beta-ribbon followed by an alpha-helix. The two doubly linked beta50/beta61 chromophores (one on each beta subunit) are in van der Waals contact, suggesting that exciton-coupling mechanisms may alter their spectral properties. Each alpha subunit carries a covalently linked 15,16-dihydrobiliverdin chromophore that is likely to be the final energy acceptor. The architecture of the heterodimer suggests that PE 545 may dock to an acceptor protein via a deep cleft and that energy may be transferred via this intermediary protein to the reaction center.


    Related Citations: 
    • Phycobilins of Cryptophycean Algae. Occurance of Dihydrobiliverdin and Mesobiliverdin in Cryptomonad Biliproteins.
      Wedemayer, G.J., Kidd, D.G., Wemmer, D.E., Glazer, A.N.
      (1992) J Biol Chem 267: 7315

    Organizational Affiliation

    Initiative in Biomolecular Structure, School of Physics, University of New South Wales, Sydney, NSW 2052, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN))
A
76Rhodomonas sp. CS24Mutation(s): 1 
Gene Names: cpeA3
Find proteins for Q00433 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  Q00433
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN))
B
67Rhodomonas sp. CS24Mutation(s): 1 
Gene Names: cpeA2
Find proteins for P30943 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  P30943
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
C, D
177Rhodomonas sp. CS24Mutation(s): 1 
Gene Names: cpeB
Find proteins for P27198 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  P27198
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download CCD File 
C, D
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
DBV
Query on DBV

Download CCD File 
A, B
15,16-DIHYDROBILIVERDIN
C33 H36 N4 O6
ZQHDSLZHMAUUQK-ZTYGKHTCSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LYZ
Query on LYZ
AL-PEPTIDE LINKINGC6 H14 N2 O3LYS
MEN
Query on MEN
C,DL-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.03α = 90
b = 82.63β = 90
c = 89.55γ = 90
Software Package:
Software NamePurpose
AMoREphasing
ARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Advisory, Data collection