1XF6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.116 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.jmb.2004.09.044
  • Primary Citation of Related Structures:  
    1XF6, 1XG0

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin alpha-3 chain76Rhodomonas sp. CS24Mutation(s): 1 
UniProt
Find proteins for Q00433 (Rhodomonas sp. (strain CS 24))
Explore Q00433 
Go to UniProtKB:  Q00433
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00433
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin alpha-2 chain67Rhodomonas sp. CS24Mutation(s): 0 
UniProt
Find proteins for P30943 (Rhodomonas sp. (strain CS 24))
Explore P30943 
Go to UniProtKB:  P30943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30943
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
B-phycoerythrin beta chain
C, D
177Rhodomonas sp. CS24Mutation(s): 1 
UniProt
Find proteins for P27198 (Rhodomonas sp. (strain CS 24))
Explore P27198 
Go to UniProtKB:  P27198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27198
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download Ideal Coordinates CCD File 
I [auth C]
J [auth C]
K [auth C]
M [auth D]
N [auth D]
I [auth C],
J [auth C],
K [auth C],
M [auth D],
N [auth D],
O [auth D]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
DBV
Query on DBV

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B]
15,16-DIHYDROBILIVERDIN
C33 H36 N4 O6
ZQHDSLZHMAUUQK-ZTYGKHTCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
LYZ
Query on LYZ
A
L-PEPTIDE LINKINGC6 H14 N2 O3LYS
MEN
Query on MEN
C, D
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.116 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.98α = 90
b = 82.555β = 90
c = 89.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description