8OV5

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

Starting Model: experimental
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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 Å). For better comparison, we improved the reference structure of this protein from Amphidinium carterae to a resolution of 1.15 Å. 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-chlorophyll a-binding protein 1, chloroplasticA [auth M],
B [auth N],
C [auth O]
312Amphidinium carteraeMutation(s): 0 
UniProt
Find proteins for P80484 (Amphidinium carterae)
Explore P80484 
Go to UniProtKB:  P80484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80484
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W4I (Subject of Investigation/LOI)
Query on W4I

Download Ideal Coordinates CCD File 
BA [auth N]
J [auth M]
JA [auth O]
O [auth M]
OA [auth O]
BA [auth N],
J [auth M],
JA [auth O],
O [auth M],
OA [auth O],
W [auth N]
[(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] (5~{Z},8~{Z},11~{Z},14~{Z},17~{Z})-icosa-5,8,11,14,17-pentaenoate
C53 H82 O15
NCMDMZMGJSDWGY-ZKVZYNAYSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
D [auth M]
DA [auth O]
E [auth M]
EA [auth O]
Q [auth N]
D [auth M],
DA [auth O],
E [auth M],
EA [auth O],
Q [auth N],
R [auth N]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PID (Subject of Investigation/LOI)
Query on PID

Download Ideal Coordinates CCD File 
AA [auth N]
F [auth M]
FA [auth O]
G [auth M]
GA [auth O]
AA [auth N],
F [auth M],
FA [auth O],
G [auth M],
GA [auth O],
H [auth M],
HA [auth O],
I [auth M],
IA [auth O],
K [auth M],
KA [auth O],
L [auth M],
LA [auth O],
M,
MA [auth O],
N [auth M],
NA [auth O],
S [auth N],
T [auth N],
U [auth N],
V [auth N],
X [auth N],
Y [auth N],
Z [auth N]
PERIDININ
C39 H50 O7
UYRDHEJRPVSJFM-FROCQLDGSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
CA [auth N],
P [auth M],
PA [auth O]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.14α = 90
b = 115.61β = 94.97
c = 65.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

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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