8EL3

Light harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in a loose interface filament


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii.

Rathbone, H.W.Laos, A.J.Michie, K.A.Iranmanesh, H.Biazik, J.Goodchild, S.C.Thordarson, P.Green, B.R.Curmi, P.M.G.

(2023) Commun Biol 6: 1158-1158

  • DOI: https://doi.org/10.1038/s42003-023-05508-4
  • Primary Citation of Related Structures:  
    7SUT, 8EL3, 8EL4, 8EL5, 8EL6

  • PubMed Abstract: 

    Cryptophyte algae have a unique phycobiliprotein light-harvesting antenna that fills a spectral gap in chlorophyll absorption from photosystems. However, it is unclear how the antenna transfers energy efficiently to these photosystems. We show that the cryptophyte Hemiselmis andersenii expresses an energetically complex antenna comprising three distinct spectrotypes of phycobiliprotein, each composed of two αβ protomers but with different quaternary structures arising from a diverse α subunit family. We report crystal structures of the major phycobiliprotein from each spectrotype. Two-thirds of the antenna consists of open quaternary form phycobiliproteins acting as primary photon acceptors. These are supplemented by a newly discovered open-braced form (~15%), where an insertion in the α subunit produces ~10 nm absorbance red-shift. The final components (~15%) are closed forms with a long wavelength spectral feature due to substitution of a single chromophore. This chromophore is present on only one β subunit where asymmetry is dictated by the corresponding α subunit. This chromophore creates spectral overlap with chlorophyll, thus bridging the energetic gap between the phycobiliprotein antenna and the photosystems. We propose that the macromolecular organization of the cryptophyte antenna consists of bulk open and open-braced forms that transfer excitations to photosystems via this bridging closed form phycobiliprotein.


  • Organizational Affiliation

    School of Physics, The University of New South Wales, Sydney, NSW, 2052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin alpha-1 subunit
A, G, J, K
67Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for U5TBU5 (Hemiselmis andersenii)
Explore U5TBU5 
Go to UniProtKB:  U5TBU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5TBU5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin550 beta subunit
B, D, F, H
177Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for U5T8W0 (Hemiselmis andersenii)
Explore U5T8W0 
Go to UniProtKB:  U5T8W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5T8W0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycoerythrin alpha-2 subunit
C, E, I, L
62Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for U5TBJ3 (Hemiselmis andersenii)
Explore U5TBJ3 
Go to UniProtKB:  U5TBJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5TBJ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AX9
Query on AX9

Download Ideal Coordinates CCD File 
N [auth B],
R [auth D],
V [auth F],
Z [auth H]
DiCys-(15,16)-Dihydrobiliverdin
C33 H40 N4 O6
MZFCOERRVCGRTL-ZTYGKHTCSA-N
PEB
Query on PEB

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth I]
DA [auth J]
EA [auth K]
AA [auth H],
BA [auth H],
CA [auth I],
DA [auth J],
EA [auth K],
FA [auth L],
M [auth A],
O [auth B],
P [auth B],
Q [auth C],
S [auth D],
T [auth D],
U [auth E],
W [auth F],
X [auth F],
Y [auth G]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYZ
Query on LYZ
A, G, J, K
L-PEPTIDE LINKINGC6 H14 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.802α = 90
b = 76.84β = 110.732
c = 103.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP180103964
Other governmentFA2386-17-1-4101 (U.S. Air Force Office of Scientific Research through the Asian Office of Aerospace Research and Developmen)
Australian Research Council (ARC)AustraliaLE190100165

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary