8OW6

PERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 ?
  • R-Value Free: 0.171 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.163 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP).

Schulte, T.Magdaong, N.C.M.Di Valentin, M.Agostini, A.Tait, C.E.Niedzwiedzki, D.M.Carbonera, D.Hofmann, E.

(2024) Biochim Biophys Acta Bioenerg 1866: 149510-149510

  • DOI: https://doi.org/10.1016/j.bbabio.2024.149510
  • Primary Citation of Related Structures:  
    8OV5, 8OW6

  • PubMed Abstract: 

    Light harvesting proteins are optimized to efficiently collect and transfer light energy for photosynthesis. In eukaryotic dinoflagellates these complexes utilize chlorophylls and a special carotenoid, peridinin, and arrange them for efficient excitation energy transfer. At the same time, the carotenoids protect the system by quenching harmful chlorophyll triplet states. Here we use advanced spectroscopic techniques and X-ray structure analysis to investigate excitation energy transfer processes in the major soluble antenna, the peridinin chlorophyll a protein (PCP) from the free living dinoflagellate Heterocapsa pygmaea. We determined the 3D-structure of this complex at high resolution (1.2??). For better comparison, we improved the reference structure of this protein from Amphidinium carterae to a resolution of 1.15??. We then used fs and ns time-resolved absorption spectroscopy to study the mechanisms of light harvesting, but also of the photoprotective quenching of the chlorophyll triplet state. The photoprotection site was further characterized by Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy to yield information on water molecules involved in triplet-triplet energy transfer. Similar to other PCP complexes, excitation energy transfer from peridinin to chlorophyll is found to be very efficient, with transfer times in the range of 1.6-2.1?ps. One of the four carotenoids, the peridinin 614, is well positioned to quench the chlorophyll triplet state with high efficiency and transfer times in the range of tens of picoseconds. Our structural and dynamic data further support, that the intrinsic water molecule coordinating the chlorophyll Mg ion plays an essential role in photoprotection.


  • Organizational Affiliation

    Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, 17121 Solna, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peridinin-chl a protein
A, C
149Heterocapsa pygmaeaMutation(s): 0 
UniProt
Find proteins for Q9FEY4 (Heterocapsa pygmaea)
Explore Q9FEY4 
Go to UniProtKB:  Q9FEY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FEY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peridinin-chl a protein
B, D
149Heterocapsa pygmaeaMutation(s): 0 
UniProt
Find proteins for Q9FEY4 (Heterocapsa pygmaea)
Explore Q9FEY4 
Go to UniProtKB:  Q9FEY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FEY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W4O (Subject of Investigation/LOI)
Query on W4O

Download Ideal Coordinates CCD File 
FA [auth D],
J [auth A],
R [auth B],
Z [auth C]
[(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoate
C51 H80 O15
VXOQBABFAYTJKD-LAAVQGTGSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
M [auth B],
U [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PID (Subject of Investigation/LOI)
Query on PID

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
F [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
PERIDININ
C39 H50 O7
UYRDHEJRPVSJFM-FROCQLDGSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
L [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
K [auth A],
S [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
T [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A, C
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 ?
  • R-Value Free: 0.171 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.163 
  • Space Group: P 3 1 2
Unit Cell:
Length ( ? )Angle ( ? )
a = 90.61¦Á = 90
b = 90.61¦Â = 90
c = 155.61¦Ã = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB480

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary
  • Version 1.2: 2024-10-16
    Changes: Database references
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