7SUT | pdb_00007sut

Light harvesting phycobiliprotein HaPE645 from the cryptophyte Hemiselmis andersenii CCMP644


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.175 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 117.22 kDa 
  • Atom Count: 8,651 
  • Modeled Residue Count: 954 
  • Deposited Residue Count: 1,004 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HaPE645 alpha-1 subunit
A, E
80Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for A0A7S0U215 (Hemiselmis andersenii)
Explore A0A7S0U215 
Go to UniProtKB:  A0A7S0U215
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S0U215
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HaPE645 alpha-2 subunit
C, G
68Hemiselmis anderseniiMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X2I
(Subject of Investigation/LOI)

Query on X2I



Download:Ideal Coordinates CCD File
I [auth A],
P [auth C],
T [auth E],
X [auth G]
(15,16)-DIHYDROBILIVERDIN (SINGLY LINKED)
C33 H40 N4 O6
VPVJAAZCMDJQMG-WLUDIELQSA-N
CYC
(Subject of Investigation/LOI)

Query on CYC



Download:Ideal Coordinates CCD File
R [auth D],
Z [auth H]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
PEB
(Subject of Investigation/LOI)

Query on PEB



Download:Ideal Coordinates CCD File
AA [auth H]
M [auth B]
N [auth B]
S [auth D]
V [auth F]
AA [auth H],
M [auth B],
N [auth B],
S [auth D],
V [auth F],
W [auth F]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
AX9
(Subject of Investigation/LOI)

Query on AX9



Download:Ideal Coordinates CCD File
L [auth B],
Q [auth D],
U [auth F],
Y [auth H]
DiCys-(15,16)-Dihydrobiliverdin
C33 H40 N4 O6
MZFCOERRVCGRTL-ZTYGKHTCSA-N
BTB

Query on BTB



Download:Ideal Coordinates CCD File
O [auth B]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
BA [auth H],
J [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.175 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.032α = 90
b = 80.983β = 92.214
c = 115.837γ = 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 governmentAustraliaFA2386-17-1-4101 (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
  • Version 1.4: 2026-03-04
    Changes: Refinement description