3iis

Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP)

Method: X-RAY DIFFRACTION

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

Peridinin-chlorophyll a-binding protein 1, chloroplastic

Amphidinium carterae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLOROPHYLL A × 2 PERIDININ × 8 ;(2S)-3-[(6-O-alpha-D-galactopyranosyl-beta-D-galactopyranosyl)oxy]-2-[(3Z,6Z,9Z,12Z,15Z)-octadeca-3,6,9,12,15-pentaenoyloxy]propyl (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate ; × 2 CADMIUM ION × 8 POTASSIUM ION × 6 CHLORIDE ION × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCP1_AMPCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain M； PDBConstruct 1–151； UniProt 57–207

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	3iis
Deposition date deposition_date	2009-08-03
Structure title title	Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP)
Keywords keywords	;ALPHA HELICAL, LIGHT HARVESTING PROTEIN, PHOTOSYNTHESIS, CAROTENOIDS, DINOFLAGELLATES, Chlorophyll, Chloroplast, Chromophore, Light-harvesting polypeptide, Transit peptide ;; 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.

3iis__assembly_1__model_1

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

Download this curve (.dat)

3iis__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3iis__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.31 Å
Rg (electron density)	20.27 Å
Total Rg	21.96 Å
Atom count	2898
Residues	302
Excluded volume	54473 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3iis__assembly_1__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	Peridinin-chlorophyll a-binding protein 1, chloroplastic
Molecular weight formula_weight	15954.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M
Atom count atom_count	1910

ADEIGDAAKKLGDASYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVMGAAADPKLLKAAAEAHHKAIGSVSGPNGVTSRADWDSVNAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVNGADAEKAYEGFLAFKDVVKKSQ

Source Source

Source organism organism	Amphidinium carterae
Common name common_name	Dinoflagellate
NCBI taxonomy ID ncbi_taxonomy_id	2961
Host organism host_organism	Escherichia coli

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	1

Entity 3 Entity 3 non-polymer

Description description	PERIDININ
Molecular weight formula_weight	630.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;(2S)-3-[(6-O-alpha-D-galactopyranosyl-beta-D-galactopyranosyl)oxy]-2-[(3Z,6Z,9Z,12Z,15Z)-octadeca-3,6,9,12,15-pentaenoyloxy]propyl (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate ;
Molecular weight formula_weight	957.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3iisM00
Class class	1 — Mainly Alpha
Architecture architecture	40 — Alpha solenoid
Topology topology	10 — Peridinin-chlorophyll Protein, Chain M
Homologous superfamily homologous superfamily	10 — Peridinin-chlorophyll A binding

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Unit-cell length a length_a	68.690 Å
Unit-cell length b length_b	81.623 Å
Unit-cell length c length_c	75.080 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	35.850 Å
R factor r_factor	0.1535
R_work r_work	0.1518
R_free r_free	0.1872

Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP)

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

Peridinin-chlorophyll a-binding protein 1, 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

3iis__assembly_1__model_1

3iis__assembly_1__model_1 | I(q)

3iis__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP)

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

Peridinin-chlorophyll a-binding protein 1, 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

3iis__assembly_1__model_1

3iis__assembly_1__model_1 | I(q)

3iis__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)