1XG0

High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy

Doust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.

(2004) J.Mol.Biol. 344: 135-153

  • DOI: 10.1016/j.jmb.2004.09.044
  • Primary Citation of Related Structures:  1XF6

  • PubMed Abstract: 
  • Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein p ...

    Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (PE545). The ultrahigh resolution crystal structure of PE545, isolated from a unicellular cryptophyte Rhodomonas CS24, is reported at both 1.1A and 0.97A resolution, revealing details of the conformation and environments of the chromophores. Absorption, emission and polarized steady state spectroscopy (298K, 77K), as well as ultrafast (20fs time resolution) measurements of population dynamics are reported. Coupled with complementary quantum chemical calculations of electronic transitions of the bilins, these enable assignment of spectral absorption characteristics to each chromophore in the structure. Spectral differences between the tetrapyrrole pigments due to chemical differences between bilins, as well as their binding and interaction with the local protein environment are described. Based on these assignments, and considering customized optical properties such as strong coupling, a model for light harvesting by PE545 is developed which explains the fast, directional harvesting of excitation energy. The excitation energy is funnelled from four peripheral pigments (beta158,beta82) into a central chromophore dimer (beta50/beta61) in approximately 1ps. Those chromophores, in turn, transfer the excitation energy to the red absorbing molecules located at the periphery of the complex in approximately 4ps. A final resonance energy transfer step sensitizes just one of the alpha19 bilins on a time scale of 22ps. Furthermore, it is concluded that binding of PE545 to the thylakoid membrane is not essential for efficient energy transfer to the integral membrane chlorophyll a-containing complexes associated with PS-II.


    Related Citations: 
    • Phycobilins of cryptophycean algae. Occurrence 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
    • 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.G.
      (1999) Proc.Natl.Acad.Sci.Usa 96: 8901


    Organizational Affiliation

    Lash-Miller Chemical Laboratories, University of Toronto, 80 St George Street, Toronto, Ontario, Canada M5S 3H6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin alpha-3 chain
A
76Rhodomonas sp. (strain CS 24)Gene Names: cpeA3
Find proteins for Q00433 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  Q00433
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin alpha-2 chain
B
67Rhodomonas sp. (strain CS 24)Gene Names: cpeA2
Find proteins for P30943 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  P30943
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
B-phycoerythrin beta chain
C, D
177Rhodomonas sp. (strain CS 24)Gene Names: cpeB
Find proteins for P27198 (Rhodomonas sp. (strain CS 24))
Go to UniProtKB:  P27198
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

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

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.980α = 90.00
b = 82.764β = 90.00
c = 89.477γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance