2BHW

PEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanisms of Photoprotection and Nonphotochemical Quenching in Pea Light-Harvesting Complex at 2.5 A Resolution.

Standfuss, J.Terwisscha Van Scheltinga, A.C.Lamborghini, M.Kuehlbrandt, W.

(2005) EMBO J 24: 919

  • DOI: 10.1038/sj.emboj.7600585
  • Primary Citation of Related Structures:  
    2BHW

  • PubMed Abstract: 
  • The plant light-harvesting complex of photosystem II (LHC-II) collects and transmits solar energy for photosynthesis in chloroplast membranes and has essential roles in regulation of photosynthesis and in photoprotection. The 2.5 A structure of pea LHC-II determined by X-ray crystallography of stacked two-dimensional crystals shows how membranes interact to form chloroplast grana, and reveals the mutual arrangement of 42 chlorophylls a and b, 12 carotenoids and six lipids in the LHC-II trimer ...

    The plant light-harvesting complex of photosystem II (LHC-II) collects and transmits solar energy for photosynthesis in chloroplast membranes and has essential roles in regulation of photosynthesis and in photoprotection. The 2.5 A structure of pea LHC-II determined by X-ray crystallography of stacked two-dimensional crystals shows how membranes interact to form chloroplast grana, and reveals the mutual arrangement of 42 chlorophylls a and b, 12 carotenoids and six lipids in the LHC-II trimer. Spectral assignment of individual chlorophylls indicates the flow of energy in the complex and the mechanism of photoprotection in two close chlorophyll a-lutein pairs. We propose a simple mechanism for the xanthophyll-related, slow component of nonphotochemical quenching in LHC-II, by which excess energy is transferred to a zeaxanthin replacing violaxanthin in its binding site, and dissipated as heat. Our structure shows the complex in a quenched state, which may be relevant for the rapid, pH-induced component of nonphotochemical quenching.


    Related Citations: 
    • Atomic Model of Plant Light-Harvesting Complex by Electron Crystallography
      Kuehlbrandt, W., Wang, D.N., Fujiyoshi, Y.
      (1994) Nature 367: 614

    Organizational Affiliation

    Max Planck Institute of Biophysics, Department of Structural Biology, Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHLOROPHYLL A-B BINDING PROTEIN AB80A, B, C232Pisum sativumMutation(s): 0 
Gene Names: AB80
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting Complexes
Protein: 
Light-Harvesting Complex LHC-II, Pea Photosystem II
Find proteins for P07371 (Pisum sativum)
Explore P07371 
Go to UniProtKB:  P07371
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
KB [auth C], QA [auth B], W [auth A]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CHL
Query on CHL

Download Ideal Coordinates CCD File 
DB [auth C] , EB [auth C] , FB [auth C] , GB [auth C] , HB [auth C] , IB [auth C] , JA [auth B] , KA [auth B] , 
DB [auth C],  EB [auth C],  FB [auth C],  GB [auth C],  HB [auth C],  IB [auth C],  JA [auth B],  KA [auth B],  LA [auth B],  MA [auth B],  NA [auth B],  OA [auth B],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AB [auth C] , BA [auth B] , BB [auth C] , CA [auth B] , CB [auth C] , DA [auth B] , EA [auth B] , FA [auth B] , 
AB [auth C],  BA [auth B],  BB [auth C],  CA [auth B],  CB [auth C],  DA [auth B],  EA [auth B],  FA [auth B],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  VA [auth C],  WA [auth C],  XA [auth C],  YA [auth C],  ZA [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LHG
Query on LHG

Download Ideal Coordinates CCD File 
JB [auth C], PA [auth B], V [auth A]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
NEX
Query on NEX

Download Ideal Coordinates CCD File 
F [auth A], TA [auth C], Z [auth B](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
 Ligand Interaction
XAT
Query on XAT

Download Ideal Coordinates CCD File 
AA [auth B], G [auth A], UA [auth C](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
 Ligand Interaction
LUX
Query on LUX

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], RA [auth C], SA [auth C], X [auth B], Y [auth B](3R,3'R,6'S,9R,9'R,13R,13'S)-4',5'-DIDEHYDRO-5',6',7',8',9,9',10,10',11,11',12,12',13,13',14,14',15,15'-OCTADECAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H72 O2
OXVWOOPFXSSEKV-SQYYBNMASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.4α = 90
b = 128β = 101.8
c = 62γ = 90
Software Package:
Software NamePurpose
TNTrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-24
    Changes: Advisory, Data collection, Other