2BHW

PEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2BHW/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Pisum sativum
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2005-01-19 Released: 2006-05-23
Deposition Author(s): Standfuss, J., Terwisscha van Scheltinga, A.C., Lamborghini, M., Kuehlbrandt, W.

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

Ligand Structure Quality Assessment

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

PubMed: 15719016 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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. 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
Modelled Residue Count: 669
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHLOROPHYLL A-B BINDING PROTEIN AB80	A, B, C	232	Pisum sativum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07371 (Pisum sativum) Explore P07371 Go to UniProtKB: P07371
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07371
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download Ideal Coordinates CCD File SDF format, chain KB [auth C] SDF format, chain QA [auth B] SDF format, chain W [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain W [auth A]	KB [auth C], QA [auth B], W [auth A]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain KB [auth C] Focus chain QA [auth B] Focus chain W [auth A] Interactions & Density Focus chain KB [auth C] Focus chain QA [auth B] Focus chain W [auth A]
CHL Query on CHL Download Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	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		Interactions Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain FA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain FA [auth B]	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		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain JB [auth C] SDF format, chain PA [auth B] SDF format, chain V [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain V [auth A]	JB [auth C], PA [auth B], V [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain JB [auth C] Focus chain PA [auth B] Focus chain V [auth A] Interactions & Density Focus chain JB [auth C] Focus chain PA [auth B] Focus chain V [auth A]
XAT Query on XAT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain UA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain UA [auth C]	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		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain UA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain UA [auth C]
NEX Query on NEX Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain TA [auth C] SDF format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain Z [auth B]	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		Interactions Focus chain F [auth A] Focus chain TA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain F [auth A] Focus chain TA [auth C] Focus chain Z [auth B]
LUX Query on LUX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain X [auth B] Focus chain Y [auth B]