3PL9

Crystal structure of spinach minor light-harvesting complex CP29 at 2.80 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


Literature

Structural insights into energy regulation of light-harvesting complex CP29 from spinach.

Pan, X.Li, M.Wan, T.Wang, L.Jia, C.Hou, Z.Zhao, X.Zhang, J.Chang, W.

(2011) Nat Struct Mol Biol 18: 309-315

  • DOI: https://doi.org/10.1038/nsmb.2008
  • Primary Citation of Related Structures:  
    3PL9

  • PubMed Abstract: 

    CP29, one of the minor light-harvesting complexes of higher-plant photosystem II, absorbs and transfers solar energy for photosynthesis and also has important roles in photoprotection. We have solved the crystal structure of spinach CP29 at 2.80-Å resolution. Each CP29 monomer contains 13 chlorophyll and 3 carotenoid molecules, which differs considerably from the major light-harvesting complex LHCII and the previously proposed CP29 model. The 13 chlorophyll-binding sites are assigned as eight chlorophyll a sites, four chlorophyll b and one putative mixed site occupied by both chlorophylls a and b. Based on the present X-ray structure, an integrated pigment network in CP29 is constructed. Two special clusters of pigment molecules, namely a615-a611-a612-Lut and Vio(Zea)-a603-a609, have been identified and might function as potential energy-quenching centers and as the exit or entrance in energy-transfer pathways.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll A-B binding protein243Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for F2Z293 (Spinacia oleracea)
Explore F2Z293 
Go to UniProtKB:  F2Z293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z293
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
Query on CHL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
M [auth A]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
H [auth A]
I [auth A]
B [auth A],
C [auth A],
D [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
NEX
Query on NEX

Download Ideal Coordinates CCD File 
Q [auth A](1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT
Query on XAT

Download Ideal Coordinates CCD File 
P [auth A](3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

Download Ideal Coordinates CCD File 
O [auth A](3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
HTG
Query on HTG

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
G3P
Query on G3P

Download Ideal Coordinates CCD File 
R [auth A]SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.793α = 90
b = 68.793β = 90
c = 425.778γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-05-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-25
    Changes: Database references
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2024-03-20
    Changes: Data collection, Database references, Non-polymer description, Structure summary