8HG6

Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri

PDB DOI: https://doi.org/10.2210/pdb8HG6/pdb
EM Map EMD-34736: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Ostreococcus tauri
Expression System: Ostreococcus tauri
Mutation(s): No

Deposited: 2022-11-13 Released: 2023-04-26
Deposition Author(s): Shan, J., Sheng, X., Ishii, A., Watanabe, A., Song, C., Murata, K., Minagawa, J., Liu, Z.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers.

Ishii, A., Shan, J., Sheng, X., Kim, E., Watanabe, A., Yokono, M., Noda, C., Song, C., Murata, K., Liu, Z., Minagawa, J.

(2023) Elife 12

PubMed: 36951548 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.84488
Primary Citation of Related Structures:
7YCA, 8HG3, 8HG5, 8HG6

PubMed Abstract:
As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of Ot PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll a 603- a 609 pair in Ot Lhca1-4.

Organizational Affiliation

Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan.

Macromolecule Content

Total Structure Weight: 121.41 kDa
Atom Count: 7,259
Modelled Residue Count: 593
Deposited Residue Count: 699
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, chloroplastic	A [auth V], B [auth W], C [auth X]	233	Ostreococcus tauri	Mutation(s): 0 Gene Names: OT_ostta16g00450
UniProt
Find proteins for Q3B9U7 (Ostreococcus tauri) Explore Q3B9U7 Go to UniProtKB: Q3B9U7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3B9U7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHL Query on CHL Download Ideal Coordinates CCD File SDF format, chain BA [auth W] SDF format, chain CA [auth W] SDF format, chain DA [auth W] SDF format, chain EA [auth W] SDF format, chain G [auth V] SDF format, chain GB [auth X] SDF format, chain H [auth V] SDF format, chain I [auth V] SDF format, chain J [auth V] SDF format, chain LA [auth W] SDF format, chain Q [auth V] SDF format, chain WA [auth X] SDF format, chain XA [auth X] SDF format, chain YA [auth X] SDF format, chain ZA [auth X] MOL2 format, chain BA [auth W] MOL2 format, chain CA [auth W] MOL2 format, chain DA [auth W] MOL2 format, chain EA [auth W] MOL2 format, chain G [auth V] MOL2 format, chain GB [auth X] MOL2 format, chain H [auth V] MOL2 format, chain I [auth V] MOL2 format, chain J [auth V] MOL2 format, chain LA [auth W] MOL2 format, chain Q [auth V] MOL2 format, chain WA [auth X] MOL2 format, chain XA [auth X] MOL2 format, chain YA [auth X] MOL2 format, chain ZA [auth X]	BA [auth W] CA [auth W] DA [auth W] EA [auth W] G [auth V] BA [auth W], CA [auth W], DA [auth W], EA [auth W], G [auth V], GB [auth X], H [auth V], I [auth V], J [auth V], LA [auth W], Q [auth V], WA [auth X], XA [auth X], YA [auth X], ZA [auth X]	CHLOROPHYLL B C₅₅ H₇₀ Mg N₄ O₆ MWVCRINOIIOUAU-UYSPMESUSA-M		Interactions Focus chain BA [auth W] Focus chain CA [auth W] Focus chain DA [auth W] Focus chain EA [auth W] Focus chain G [auth V] Focus chain GB [auth X] Focus chain H [auth V] Focus chain I [auth V] Focus chain J [auth V] Focus chain LA [auth W] Focus chain Q [auth V] Focus chain WA [auth X] Focus chain XA [auth X] Focus chain YA [auth X] Focus chain ZA [auth X] Interactions & Density Focus chain BA [auth W] Focus chain CA [auth W] Focus chain DA [auth W] Focus chain EA [auth W] Focus chain G [auth V] Focus chain GB [auth X] Focus chain H [auth V] Focus chain I [auth V] Focus chain J [auth V] Focus chain LA [auth W] Focus chain Q [auth V] Focus chain WA [auth X] Focus chain XA [auth X] Focus chain YA [auth X] Focus chain ZA [auth X]
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain AA [auth W] SDF format, chain BB [auth X] SDF format, chain CB [auth X] SDF format, chain D [auth V] SDF format, chain DB [auth X] SDF format, chain E [auth V] SDF format, chain EB [auth X] SDF format, chain F [auth V] SDF format, chain FB [auth X] SDF format, chain GA [auth W] SDF format, chain HA [auth W] SDF format, chain IA [auth W] SDF format, chain JA [auth W] SDF format, chain KA [auth W] SDF format, chain L [auth V] SDF format, chain M [auth V] SDF format, chain N [auth V] SDF format, chain O [auth V] SDF format, chain P [auth V] SDF format, chain TA [auth X] SDF format, chain UA [auth X] SDF format, chain VA [auth X] SDF format, chain Y [auth W] SDF format, chain Z [auth W] MOL2 format, chain AA [auth W] MOL2 format, chain BB [auth X] MOL2 format, chain CB [auth X] MOL2 format, chain D [auth V] MOL2 format, chain DB [auth X] MOL2 format, chain E [auth V] MOL2 format, chain EB [auth X] MOL2 format, chain F [auth V] MOL2 format, chain FB [auth X] MOL2 format, chain GA [auth W] MOL2 format, chain HA [auth W] MOL2 format, chain IA [auth W] MOL2 format, chain JA [auth W] MOL2 format, chain KA [auth W] MOL2 format, chain L [auth V] MOL2 format, chain M [auth V] MOL2 format, chain N [auth V] MOL2 format, chain O [auth V] MOL2 format, chain P [auth V] MOL2 format, chain TA [auth X] MOL2 format, chain UA [auth X] MOL2 format, chain VA [auth X] MOL2 format, chain Y [auth W] MOL2 format, chain Z [auth W]	AA [auth W] BB [auth X] CB [auth X] D [auth V] DB [auth X] AA [auth W], BB [auth X], CB [auth X], D [auth V], DB [auth X], E [auth V], EB [auth X], F [auth V], FB [auth X], GA [auth W], HA [auth W], IA [auth W], JA [auth W], KA [auth W], L [auth V], M [auth V], N [auth V], O [auth V], P [auth V], TA [auth X], UA [auth X], VA [auth X], Y [auth W], Z [auth W]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth W] Focus chain BB [auth X] Focus chain CB [auth X] Focus chain D [auth V] Focus chain DB [auth X] Focus chain E [auth V] Focus chain EB [auth X] Focus chain F [auth V] Focus chain FB [auth X] Focus chain GA [auth W] Focus chain HA [auth W] Focus chain IA [auth W] Focus chain JA [auth W] Focus chain KA [auth W] Focus chain L [auth V] Focus chain M [auth V] Focus chain N [auth V] Focus chain O [auth V] Focus chain P [auth V] Focus chain TA [auth X] Focus chain UA [auth X] Focus chain VA [auth X] Focus chain Y [auth W] Focus chain Z [auth W] Interactions & Density Focus chain AA [auth W] Focus chain BB [auth X] Focus chain CB [auth X] Focus chain D [auth V] Focus chain DB [auth X] Focus chain E [auth V] Focus chain EB [auth X] Focus chain F [auth V] Focus chain FB [auth X] Focus chain GA [auth W] Focus chain HA [auth W] Focus chain IA [auth W] Focus chain JA [auth W] Focus chain KA [auth W] Focus chain L [auth V] Focus chain M [auth V] Focus chain N [auth V] Focus chain O [auth V] Focus chain P [auth V] Focus chain TA [auth X] Focus chain UA [auth X] Focus chain VA [auth X] Focus chain Y [auth W] Focus chain Z [auth W]
KC2 (Subject of Investigation/LOI) Query on KC2 Download Ideal Coordinates CCD File SDF format, chain AB [auth X] SDF format, chain FA [auth W] SDF format, chain K [auth V] MOL2 format, chain AB [auth X] MOL2 format, chain FA [auth W] MOL2 format, chain K [auth V]	AB [auth X], FA [auth W], K [auth V]	Chlorophyll c2 C₃₅ H₂₈ Mg N₄ O₅ QDRBYWCRXZZVLY-QIEHNWLWSA-L		Interactions Focus chain AB [auth X] Focus chain FA [auth W] Focus chain K [auth V] Interactions & Density Focus chain AB [auth X] Focus chain FA [auth W] Focus chain K [auth V]
NEX Query on NEX Download Ideal Coordinates CCD File SDF format, chain OA [auth W] MOL2 format, chain OA [auth W]	OA [auth W]	(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 OA [auth W] Interactions & Density Focus chain OA [auth W]
IWJ (Subject of Investigation/LOI) Query on IWJ Download Ideal Coordinates CCD File SDF format, chain JB [auth X] SDF format, chain PA [auth W] SDF format, chain T [auth V] SDF format, chain U [auth V] SDF format, chain W [auth V] MOL2 format, chain JB [auth X] MOL2 format, chain PA [auth W] MOL2 format, chain T [auth V] MOL2 format, chain U [auth V] MOL2 format, chain W [auth V]	JB [auth X], PA [auth W], T [auth V], U [auth V], W [auth V]	(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 JB [auth X] Focus chain PA [auth W] Focus chain T [auth V] Focus chain U [auth V] Focus chain W [auth V] Interactions & Density Focus chain JB [auth X] Focus chain PA [auth W] Focus chain T [auth V] Focus chain U [auth V] Focus chain W [auth V]
Q6L Query on Q6L Download Ideal Coordinates CCD File SDF format, chain HB [auth X] SDF format, chain IB [auth X] SDF format, chain KB [auth X] SDF format, chain MA [auth W] SDF format, chain NA [auth W] SDF format, chain QA [auth W] SDF format, chain R [auth V] SDF format, chain RA [auth W] SDF format, chain S [auth V] SDF format, chain SA [auth X] SDF format, chain V SDF format, chain X [auth V] MOL2 format, chain HB [auth X] MOL2 format, chain IB [auth X] MOL2 format, chain KB [auth X] MOL2 format, chain MA [auth W] MOL2 format, chain NA [auth W] MOL2 format, chain QA [auth W] MOL2 format, chain R [auth V] MOL2 format, chain RA [auth W] MOL2 format, chain S [auth V] MOL2 format, chain SA [auth X] MOL2 format, chain V MOL2 format, chain X [auth V]	HB [auth X] IB [auth X] KB [auth X] MA [auth W] NA [auth W] HB [auth X], IB [auth X], KB [auth X], MA [auth W], NA [auth W], QA [auth W], R [auth V], RA [auth W], S [auth V], SA [auth X], V, X [auth V]	(1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-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-octaenyl]cyclohex-3-en-1-ol C₄₀ H₅₈ O₂ ULGXMGDBVFOYRY-NBTBXAKCSA-N		Interactions Focus chain HB [auth X] Focus chain IB [auth X] Focus chain KB [auth X] Focus chain MA [auth W] Focus chain NA [auth W] Focus chain QA [auth W] Focus chain R [auth V] Focus chain RA [auth W] Focus chain S [auth V] Focus chain SA [auth X] Focus chain V Focus chain X [auth V] Interactions & Density Focus chain HB [auth X] Focus chain IB [auth X] Focus chain KB [auth X] Focus chain MA [auth W] Focus chain NA [auth W] Focus chain QA [auth W] Focus chain R [auth V] Focus chain RA [auth W] Focus chain S [auth V] Focus chain SA [auth X] Focus chain V Focus chain X [auth V]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H04778 and 21H05040
Chinese Academy of Sciences	China	XDB37020101 and YSBR-015
National Natural Science Foundation of China (NSFC)	China	31925024
Ministry of Science and Technology (MoST, China)	China	2017YFA0503702