7T89

Light harvesting complex Phycocyanin PC577 from the cryptophyte Hemiselmis pacifica CCMP 706


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins.

Michie, K.A.Harrop, S.J.Rathbone, H.W.Wilk, K.E.Teng, C.Y.Hoef-Emden, K.Hiller, R.G.Green, B.R.Curmi, P.M.G.

(2023) Protein Sci 32: e4586-e4586

  • DOI: https://doi.org/10.1002/pro.4586
  • Primary Citation of Related Structures:  
    7T7U, 7T89, 7T8S

  • PubMed Abstract: 

    In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.


  • Organizational Affiliation

    School of Physics, The University of New South Wales, Sydney, New South Wales, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin alpha subunit 1
A, C
63Hemiselmis pacificaMutation(s): 0 
UniProt
Find proteins for A0A067XP79 (Hemiselmis pacifica)
Explore A0A067XP79 
Go to UniProtKB:  A0A067XP79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067XP79
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin beta subunit
B, D
177Hemiselmis pacificaMutation(s): 0 
UniProt
Find proteins for A0A067XP89 (Hemiselmis pacifica)
Explore A0A067XP89 
Go to UniProtKB:  A0A067XP89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067XP89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AX9 (Subject of Investigation/LOI)
Query on AX9

Download Ideal Coordinates CCD File 
F [auth B],
J [auth D]
DiCys-(15,16)-Dihydrobiliverdin
C33 H40 N4 O6
MZFCOERRVCGRTL-ZTYGKHTCSA-N
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
H [auth B]
I [auth C]
K [auth D]
E [auth A],
G [auth B],
H [auth B],
I [auth C],
K [auth D],
L [auth D]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.116α = 90
b = 95.322β = 90
c = 125.577γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaARC LIEF LE190100165
Australian Research Council (ARC)AustraliaDP180103964
Other governmentUnited StatesFA2386-17-1-4101

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2023-08-09
    Changes: Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection
  • Version 1.4: 2024-10-16
    Changes: Structure summary