9UC6 | pdb_00009uc6

Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9UC6/pdb
EM Map EMD-64036: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Ostreococcus tauri
Mutation(s): No

Deposited: 2025-04-03 Released: 2025-12-31
Deposition Author(s): Seki, S., Kubota, M., Ishii, A., Kim, E., Tanaka, H., Miyata, T., Namba, K., Kurisu, G., Minagawa, J., Fujii, R.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cryo-EM structure of the LHCp trimer from Ostreococcus tauri at 1.94 angstrom resolution

Soichiro, S., Kubota, M., Ishii, A., Kim, E., Tomoko, M., Hideaki, T., Keiichi, N., Genji, K., Minagawa, J., Ritsuko, F.

To be published.

Macromolecule Content

Total Structure Weight: 119.43 kDa
Atom Count: 8,379
Modeled Residue Count: 606
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	A, B, C	202	Ostreococcus tauri	Mutation(s): 0
UniProt
Find proteins for Q3B9V0 (Ostreococcus tauri) Explore Q3B9V0 Go to UniProtKB: Q3B9V0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3B9V0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV0 Query on AV0 Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain VA [auth B] SDF format, chain SB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain SB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain SB [auth C]	SB [auth C], VA [auth B], X [auth A]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-VWHTXWAPSA-N		Interactions Focus chain SB [auth C] Focus chain VA [auth B] Focus chain X [auth A] Interactions & Density Focus chain SB [auth C] Focus chain VA [auth B] Focus chain X [auth A]
CHL (Subject of Investigation/LOI) Query on CHL Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain MB [auth C] SDF format, chain LB [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain EB [auth C] SDF format, chain E [auth A] SDF format, chain DB [auth C] SDF format, chain DA [auth B] SDF format, chain CB [auth C] SDF format, chain AB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain E [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain LB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain E [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] CB [auth C] DA [auth B] DB [auth C] E [auth A] AB [auth C], CB [auth C], DA [auth B], DB [auth C], E [auth A], EB [auth C], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], LB [auth C], MB [auth C], OA [auth B], P [auth A], PA [auth B], Q [auth A]	CHLOROPHYLL B C₅₅ H₇₀ Mg N₄ O₆ MWVCRINOIIOUAU-UYSPMESUSA-M		Interactions Focus chain AB [auth C] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain AB [auth C] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A]
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KB [auth C] SDF format, chain KA [auth B] SDF format, chain JB [auth C] SDF format, chain J [auth A] SDF format, chain IB [auth C] SDF format, chain IA [auth B] SDF format, chain HB [auth C] SDF format, chain FB [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] SDF format, chain BB [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth C]	BB [auth C] CA [auth B] D [auth A] EA [auth B] F [auth A] BB [auth C], CA [auth B], D [auth A], EA [auth B], F [auth A], FB [auth C], HB [auth C], IA [auth B], IB [auth C], J [auth A], JB [auth C], KA [auth B], KB [auth C], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], ZA [auth C]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain BB [auth C] Focus chain CA [auth B] Focus chain D [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain BB [auth C] Focus chain CA [auth B] Focus chain D [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain ZA [auth C]
SQD (Subject of Investigation/LOI) Query on SQD Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain WA [auth B] SDF format, chain TB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain TB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain TB [auth C]	TB [auth C], WA [auth B], Y [auth A]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain TB [auth C] Focus chain WA [auth B] Focus chain Y [auth A] Interactions & Density Focus chain TB [auth C] Focus chain WA [auth B] Focus chain Y [auth A]
A1LYW (Subject of Investigation/LOI) Query on A1LYW Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain XA [auth B] SDF format, chain BA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain BA [auth B]	BA [auth B], XA [auth B], Z [auth A]	[(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-7-oxabicyclo[4.1.0]heptan-3-yl] (~{Z})-oct-2-enoate C₄₈ H₆₈ O₄ RYRZHZDRYZHUCF-CKQNEJSZSA-N		Interactions Focus chain BA [auth B] Focus chain XA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth B] Focus chain XA [auth B] Focus chain Z [auth A]
A1LYY (Subject of Investigation/LOI) Query on A1LYY Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain OB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain OB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain OB [auth C]	OB [auth C], RA [auth B], S [auth A]	(5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]-5-[(2~{E},4~{E},6~{E},8~{E},10~{E},12~{E})-2,7,11-trimethyl-13-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]trideca-2,4,6,8,10,12-hexaenylidene]furan-2-one C₄₀ H₅₄ O₅ JVBLPSSXRSHBAY-OQINAPANSA-N		Interactions Focus chain OB [auth C] Focus chain RA [auth B] Focus chain S [auth A] Interactions & Density Focus chain OB [auth C] Focus chain RA [auth B] Focus chain S [auth A]
A1L0F (Subject of Investigation/LOI) Query on A1L0F Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain GB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GB [auth C]	GB [auth C], JA [auth B], K [auth A]	Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester C₃₅ H₃₀ Mg N₄ O₅ YXBIPIDDNARELO-KKNVGXODSA-L		Interactions Focus chain GB [auth C] Focus chain JA [auth B] Focus chain K [auth A] Interactions & Density Focus chain GB [auth C] Focus chain JA [auth B] Focus chain K [auth A]
IWJ (Subject of Investigation/LOI) Query on IWJ Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain R [auth A] SDF format, chain QB [auth C] SDF format, chain QA [auth B] SDF format, chain NB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain NB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain NB [auth C]	NB [auth C] QA [auth B] QB [auth C] R [auth A] TA [auth B] NB [auth C], QA [auth B], QB [auth C], R [auth A], TA [auth B], U [auth A]	(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one C₄₀ H₅₆ O₄ WOJYJHBMWRNRJG-ITGJSFTBSA-N		Interactions Focus chain NB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain TA [auth B] Focus chain U [auth A] Interactions & Density Focus chain NB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain TA [auth B] Focus chain U [auth A]
NEX Query on NEX Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain PB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain PB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain PB [auth C]	PB [auth C], SA [auth B], T [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		Interactions Focus chain PB [auth C] Focus chain SA [auth B] Focus chain T [auth A] Interactions & Density Focus chain PB [auth C] Focus chain SA [auth B] Focus chain T [auth A]
A1LYX (Subject of Investigation/LOI) Query on A1LYX Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain RB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain RB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain RB [auth C]	RB [auth C], UA [auth B], V [auth A]	(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-2-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]heptadeca-2,4,6,8,10,12,14,16-octaenal C₄₀ H₅₆ O₃ FJWGLEVADWWUFR-NJTXIUSISA-N		Interactions Focus chain RB [auth C] Focus chain UA [auth B] Focus chain V [auth A] Interactions & Density Focus chain RB [auth C] Focus chain UA [auth B] Focus chain V [auth A]
A1L0E (Subject of Investigation/LOI) Query on A1L0E Download:Ideal Coordinates CCD File SDF format, chain YA [auth C] SDF format, chain W [auth A] SDF format, chain AA [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain AA [auth A]	AA [auth A], W [auth A], YA [auth C]	(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15-octaenyl]cyclohex-3-en-1-ol C₄₀ H₅₈ O₂ BVQZFYCQXRWKGU-KTHHOQBFSA-N		Interactions Focus chain AA [auth A] Focus chain W [auth A] Focus chain YA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain W [auth A] Focus chain YA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.4.1
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121003
Japan Society for the Promotion of Science (JSPS)	Japan	K23KJ1834
Japan Science and Technology	Japan	JPMJFS2138
Japan Science and Technology	Japan	JPMJCR20E1
Japan Society for the Promotion of Science (JSPS)	Japan	23H04958
Japan Society for the Promotion of Science (JSPS)	Japan	21H05040
Japan Society for the Promotion of Science (JSPS)	Japan	23H04960

Revision History (Full details and data files)

Version 1.0: 2025-12-31
Type: Initial release
Version 2.0: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary