2BHW | pdb_00002bhw

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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1038/sj.emboj.7600585
  • Primary Citation 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. 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.

    • Organizational Affiliation: 
    • Max Planck Institute of Biophysics, Department of Structural Biology, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 124.67 kDa 
  • Atom Count: 8,373 
  • Modeled Residue Count: 669 
  • Deposited Residue Count: 696 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHLOROPHYLL A-B BINDING PROTEIN AB80
A, B, C
232Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07371 (Pisum sativum)
Explore P07371 
Go to UniProtKB:  P07371
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07371
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / 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
CHL

Query on CHL


Download:Ideal Coordinates CCD File
DB [auth C]
EB [auth C]
FB [auth C]
GB [auth C]
HB [auth C]
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
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth C]
BA [auth B]
BB [auth C]
CA [auth B]
CB [auth C]
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
ATNHDLDRLWWWCB-AENOIHSZSA-M
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
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
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
LUX

Query on LUX


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
RA [auth C]
SA [auth C]
X [auth B]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.241 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 2.0: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary