1rwt

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution

Method: X-RAY DIFFRACTION

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

Chlorophyll A-B binding protein, chloroplast

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	nonyl beta-D-glucopyranoside × 60 SODIUM ION × 6 (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL × 120 ;(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 ; × 60 ;(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 ; × 60 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 60 DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 60 CHLOROPHYLL B × 360 CHLOROPHYLL A × 480 water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CB21_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 36–267 Author chain B； PDBConstruct 1–232； UniProt 36–267 Author chain C； PDBConstruct 1–232； UniProt 36–267 Author chain D； PDBConstruct 1–232； UniProt 36–267 Author chain E； PDBConstruct 1–232； UniProt 36–267 Author chain F； PDBConstruct 1–232； UniProt 36–267 Author chain G； PDBConstruct 1–232； UniProt 36–267 Author chain H； PDBConstruct 1–232； UniProt 36–267 Author chain I； PDBConstruct 1–232； UniProt 36–267 Author chain J； PDBConstruct 1–232； UniProt 36–267

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	1rwt
Deposition date deposition_date	2003-12-17
Structure title title	Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution
Keywords keywords	LIGHT-HARVESTING COMPLEX, MEMBRANE PROTEIN, PLANT, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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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.

1rwt__assembly_1__model_1

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

Download this curve (.dat)

1rwt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rwt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	110.00 Å
Total Rg	110.00 Å
Atom count	170036
Residues	13086
Excluded volume	3243400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rwt__assembly_1__model_1`	60-meric （60）	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 (11)

Entity 1 Entity 1 polymer

Description description	Chlorophyll A-B binding protein, chloroplast
Molecular weight formula_weight	25000.3 kDa
Source method src_method	nat
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	29039

RKTAGKPKTVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPGK

Entity 2 Entity 2 non-polymer

Description description	nonyl beta-D-glucopyranoside
Molecular weight formula_weight	306.4 kDa
Source method src_method	man
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 5 Entity 5 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	600.9 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 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	10

Entity 7 Entity 7 non-polymer

Description description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Molecular weight formula_weight	723.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 8 Entity 8 non-polymer

Description description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
Molecular weight formula_weight	949.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 9 Entity 9 non-polymer

Description description	CHLOROPHYLL B
Molecular weight formula_weight	907.5 kDa
Source method src_method	syn
Copy count entity_count	60

Entity 10 Entity 10 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	80

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	699

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1rwta_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwte_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwth_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwti_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

Domain ID domain_id	d1rwtj_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.43 — Chlorophyll a-b binding protein
Superfamily Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
Family Family family	f.43.1.1 — Chlorophyll a-b binding protein

CATH v4.4 (10 domains)

Domain ID domain_id	1rwtA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

Domain ID domain_id	1rwtJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3460 — Chlorophyll a-b binding protein
Homologous superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

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Unit-cell length a length_a	261.787 Å
Unit-cell length b length_b	261.787 Å
Unit-cell length c length_c	660.498 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	180

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2210

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution

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

Chlorophyll A-B binding protein, chloroplast

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

1rwt__assembly_1__model_1

1rwt__assembly_1__model_1 | I(q)

1rwt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (11)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution

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

Chlorophyll A-B binding protein, chloroplast

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

1rwt__assembly_1__model_1

1rwt__assembly_1__model_1 | I(q)

1rwt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (11)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)