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

Starting Model: other
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wwPDB Validation 3D Report Full Report

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

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] mmCIF format, chain KB [auth C] mmCIF format, chain QA [auth B] mmCIF 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] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF 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 EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain VA [auth C] SDF format, chain ZA [auth C] SDF format, chain DA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] 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 EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C]	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] mmCIF format, chain JB [auth C] mmCIF format, chain PA [auth B] mmCIF 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] mmCIF format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF 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] mmCIF format, chain F [auth A] mmCIF format, chain TA [auth C] mmCIF 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] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain X [auth B] mmCIF 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]

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 = 211.4	α = 90
b = 128	β = 101.8
c = 62	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Standfuss, J.

Terwisscha van Scheltinga, A.C.

Lamborghini, M.

Kuehlbrandt, W.

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