3PL9 | pdb_00003pl9

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

• PDB DOI: https://doi.org/10.2210/pdb3PL9/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Spinacia oleracea
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2010-11-14 Released: 2011-02-09 
• Deposition Author(s): Pan, X.W., Li, M., Wan, T., Wang, L.F., Jia, C.J., Hou, Z.Q., Zhao, X.L., Zhang, J.P., Chang, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.293 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.282 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

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

• PubMed: 21297637 
• DOI: https://doi.org/10.1038/nsmb.2008
• Primary Citation 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.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.94 kDa 
• Atom Count: 2,317 
• Modeled Residue Count: 156 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll A-B binding protein	A	243	Spinacia oleracea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for F2Z293 (Spinacia oleracea) Explore F2Z293  Go to UniProtKB:  F2Z293

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHL	E [auth A], F [auth A], G [auth A], M [auth A]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	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	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	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	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	S [auth A], T [auth A]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
G3P	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 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.282 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.793	α = 90
b = 68.793	β = 90
c = 425.778	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Pan, X.W., Li, M., Wan, T., Wang, L.F., Jia, C.J., Hou, Z.Q., Zhao, X.L., Zhang, J.P., Chang, W.R.

Revision History  

• 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