9uc6

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorophyll a-b binding protein, chloroplastic

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	CHLOROPHYLL A × 21 CHLOROPHYLL B × 18 Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester × 3 ;(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 ; × 6 ;(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 ; × 3 ;(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 ; × 3 ;(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 ; × 3 ;(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 ; × 3 Lauryl Maltose Neopentyl Glycol × 3 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ;[(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 ; × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3B9V0_OSTTA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 10–211 Author chain B； PDBConstruct 1–202； UniProt 10–211 Author chain C； PDBConstruct 1–202； UniProt 10–211

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9uc6
Deposition date deposition_date	2025-04-03
Structure title title	Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution
Keywords keywords	;LHCp, Prasinophytes, green light absorption, carotenoid, photosynthesis, Light-harvesting complex, prasinoxanthin, micromonal, dihydrolutein, uriolide, acyl-antheraxanthin, DVP. ;; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9uc6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9uc6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9uc6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.05 Å
Rg (electron density)	29.83 Å
Total Rg	31.45 Å
Atom count	8193
Residues	606
Excluded volume	152840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9uc6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Chlorophyll a-b binding protein, chloroplastic
Molecular weight formula_weight	21417.9 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8379

ADIYPEFGTYPGGGESPIIPFGSEKNAEREVIHGRWAMLGVTGAWAAENGTGIPWFTAGTLCTPDDCTAVADKFPGAVAPLAPEGSGYPSFWNVLIIEIVLVGAAEAYRTGISDSPFDDGLTVGDVNPGGRFDPLGLAESGDLEELKIKELKHCRLSMFAWLGCIFQALATQEGPIANWQSHVADPVHSNVLTNAAKGFGFY

Entity 2 Entity 2 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 non-polymer

Description description	CHLOROPHYLL B
Molecular weight formula_weight	907.5 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 non-polymer

Description description	Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester
Molecular weight formula_weight	610.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	600.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	614.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	600.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	584.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	570.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	Lauryl Maltose Neopentyl Glycol
Molecular weight formula_weight	1005.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Molecular weight formula_weight	795.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 12 Entity 12 non-polymer

Description description	;[(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 ;
Molecular weight formula_weight	709.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	186

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	1.94 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1153594

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorophyll a-b binding protein, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9uc6__assembly_1__model_1

9uc6__assembly_1__model_1 | I(q)

9uc6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chlorophyll a-b binding protein, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9uc6__assembly_1__model_1

9uc6__assembly_1__model_1 | I(q)

9uc6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)