SAXSdb — 1f8v

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

MATURE CAPSID PROTEIN BETA

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 360 RNA 60	RNA × 60 CALCIUM ION × 60 SULFATE ION × 60 water × 360	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 6 RNA 1	RNA × 1 CALCIUM ION × 1 SULFATE ION × 1 water × 6	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 30 RNA 5	RNA × 5 CALCIUM ION × 5 SULFATE ION × 5 water × 30	Consistent with all polymers
4	Protein–RNA	Homooligomer	Protein 36 RNA 6	RNA × 6 CALCIUM ION × 6 SULFATE ION × 6 water × 36	Consistent with all polymers
5	Protein–RNA	Homooligomer	Protein 6 RNA 1	RNA × 1 CALCIUM ION × 1 SULFATE ION × 1 water × 6	Consistent with all polymers
6	Protein–RNA	Homooligomer	Protein 360 RNA 60	RNA × 60 CALCIUM ION × 60 SULFATE ION × 60 water × 360	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COAT_PAV
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 7–361 Author chain B； PDBConstruct 1–355； UniProt 7–361 Author chain C； PDBConstruct 1–355； UniProt 7–361 Author chain D； PDBConstruct 1–40； UniProt 362–401 Author chain E； PDBConstruct 1–40； UniProt 362–401 Author chain F； PDBConstruct 1–40； UniProt 362–401

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	1f8v
Deposition date deposition_date	2000-07-05
Structure title title	THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA
Keywords keywords	;nodavirus, coat protein, nucleoprotein, protein-RNA interactions, RNA duplex, RNA cage, gamma polypeptide, beta-sandwich, Icosahedral virus, Virus-RNA COMPLEX ;; Virus/RNA
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.

1f8v__assembly_1__model_1

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

Download this curve (.dat)

1f8v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f8v__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)	134.50 Å
Total Rg	134.20 Å
Atom count	510000
Residues	64440
Excluded volume	8974900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f8v__assembly_1__model_1`	420-MERIC （420）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1f8v__assembly_2__model_1`	heptameric （7）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1f8v__assembly_3__model_1`	35-meric （35）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1f8v__assembly_4__model_1`	42-meric （42）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1f8v__assembly_5__model_1`	heptameric （7）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1f8v__assembly_6__model_1`	420-meric （420）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	RNA
Molecular weight formula_weight	7701.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R
Atom count atom_count	8719

UUUUUUUUUUUUUAAAAUUUUUUUU

Entity 2 Entity 2 polymer

Description description	MATURE CAPSID PROTEIN BETA
Molecular weight formula_weight	38432.5 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

NRRNKARKVVSRSTALVPMAPASQRTGPAPRKPRKRNQALVRNPRLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN

Entity 3 Entity 3 polymer

Description description	MATURE CAPSID PROTEIN GAMMA
Molecular weight formula_weight	4248.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

SKFWEGVLRVLNQISGTLSVIPGPVGTISAGVHQLTGMYM

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1f8v.1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.4 — Nodaviridae-like VP

Domain ID domain_id	d1f8v.2
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.4 — Nodaviridae-like VP

Domain ID domain_id	d1f8v.3
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.4 — Nodaviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id	1f8vA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1f8vB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1f8vC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	329.332 Å
Unit-cell length b length_b	346.944 Å
Unit-cell length c length_c	424.893 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	360

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2180
R_work r_work	0.2190
R_free r_free	0.2210

THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA

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

MATURE CAPSID PROTEIN BETA

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

1f8v__assembly_1__model_1

1f8v__assembly_1__model_1 | I(q)

1f8v__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA

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

MATURE CAPSID PROTEIN BETA

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

1f8v__assembly_1__model_1

1f8v__assembly_1__model_1 | I(q)

1f8v__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)