7T8S

Light Harvesting complex phycoerythrin PE 566, from the cryptophyte Cryptomonas pyrenoidifera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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 beta subunit
A, C, E, G, I
A, C, E, G, I, K, M, O
178Cryptomonas pyrenoidiferaMutation(s): 0 
UniProt
Find proteins for A0A222AH92 (Cryptomonas curvata)
Explore A0A222AH92 
Go to UniProtKB:  A0A222AH92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A222AH92
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
phycoerythrin alpha-1 subunit
B, F, J, N
78Cryptomonas pyrenoidiferaMutation(s): 0 
UniProt
Find proteins for A0A7S0TJJ1 (Hemiselmis andersenii)
Explore A0A7S0TJJ1 
Go to UniProtKB:  A0A7S0TJJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S0TJJ1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
phycoerythrin alpha-2 subunit
D, H, L, P
70Cryptomonas pyrenoidiferaMutation(s): 0 
UniProt
Find proteins for A0A7S0UC19 (Hemiselmis andersenii)
Explore A0A7S0UC19 
Go to UniProtKB:  A0A7S0UC19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S0UC19
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KQ6 (Subject of Investigation/LOI)
Query on KQ6

Download Ideal Coordinates CCD File 
CA [auth E]
DB [auth O]
HA [auth G]
NA [auth I]
S [auth A]
CA [auth E],
DB [auth O],
HA [auth G],
NA [auth I],
S [auth A],
TA [auth K],
XA [auth M],
Y [auth C]
Bilin 584 (doubly linked)
C33 H40 N4 O6
KXOMFZIVZHIPRO-GUEBWASOSA-N
PEB (Subject of Investigation/LOI)
Query on PEB

Download Ideal Coordinates CCD File 
AA [auth E]
BB [auth O]
FA [auth G]
LA [auth I]
Q [auth A]
AA [auth E],
BB [auth O],
FA [auth G],
LA [auth I],
Q [auth A],
RA [auth K],
VA [auth M],
W [auth C]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
KPX (Subject of Investigation/LOI)
Query on KPX

Download Ideal Coordinates CCD File 
BA [auth E]
CB [auth O]
GA [auth G]
MA [auth I]
R [auth A]
BA [auth E],
CB [auth O],
GA [auth G],
MA [auth I],
R [auth A],
SA [auth K],
WA [auth M],
X [auth C]
Bilin 584 (single linked)
C33 H38 N4 O6
DELSVXYVYXKOJW-GUEBWASOSA-N
KP9 (Subject of Investigation/LOI)
Query on KP9

Download Ideal Coordinates CCD File 
EA [auth F]
EB [auth P]
JA [auth H]
QA [auth J]
UA [auth L]
EA [auth F],
EB [auth P],
JA [auth H],
QA [auth J],
UA [auth L],
V [auth B],
Z [auth D],
ZA [auth N]
Bilin 618 (single linked)
C33 H36 N4 O6
DWOKJMXOEBXRPB-ZHKKBVGESA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth N]
DA [auth E]
IA [auth G]
KA [auth H]
OA [auth I]
AB [auth N],
DA [auth E],
IA [auth G],
KA [auth H],
OA [auth I],
PA [auth I],
T [auth A],
U [auth A],
YA [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
A, C, E, G, I
A, C, E, G, I, K, M, O
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.359α = 90
b = 178.359β = 90
c = 173.546γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)ARC LIEF LE190100165
Australian Research Council (ARC)DP180103964
Other governmentFA2386-17-1-4101

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: 2023-10-25
    Changes: Data collection, Refinement description