3pto

Crystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex

Method: X-RAY DIFFRACTION

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

Nucleoprotein

Vesicular stomatitis Indiana virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	URANYL (VI) ION × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCAP_VSIVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–421； UniProt 2–422 Author chain B； PDBConstruct 1–421； UniProt 2–422 Author chain C； PDBConstruct 1–421； UniProt 2–422 Author chain D； PDBConstruct 1–421； UniProt 2–422 Author chain E； PDBConstruct 1–421； UniProt 2–422

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	3pto
Deposition date deposition_date	2010-12-03
Structure title title	Crystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex
Keywords keywords	nucleocapsid, VIRAL PROTEIN; VIRAL PROTEIN
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.

3pto__assembly_1__model_1

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

Download this curve (.dat)

3pto__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pto__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.89 Å
Rg (electron density)	58.32 Å
Total Rg	58.55 Å
Atom count	32934
Residues	4150
Excluded volume	588910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pto__assembly_1__model_1`	decameric （10）	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 (2)

Entity 1 Entity 1 polymer

Description description	Nucleoprotein
Molecular weight formula_weight	47332.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	16467

SVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGLTNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRAVMSLQGLREKTIGKYAKSEFDK

Source Source

Source organism organism	Vesicular stomatitis Indiana virus
Common name common_name	VSIV
NCBI taxonomy ID ncbi_taxonomy_id	11277
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URANYL (VI) ION
Molecular weight formula_weight	270.0 kDa
Source method src_method	syn
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3ptoa_
Class class	a — All alpha proteins
Fold Fold fold	a.260 — Rhabdovirus nucleoprotein-like
Superfamily Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
Family Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

Domain ID domain_id	d3ptob_
Class class	a — All alpha proteins
Fold Fold fold	a.260 — Rhabdovirus nucleoprotein-like
Superfamily Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
Family Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

Domain ID domain_id	d3ptoc_
Class class	a — All alpha proteins
Fold Fold fold	a.260 — Rhabdovirus nucleoprotein-like
Superfamily Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
Family Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

Domain ID domain_id	d3ptod_
Class class	a — All alpha proteins
Fold Fold fold	a.260 — Rhabdovirus nucleoprotein-like
Superfamily Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
Family Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

Domain ID domain_id	d3ptoe_
Class class	a — All alpha proteins
Fold Fold fold	a.260 — Rhabdovirus nucleoprotein-like
Superfamily Superfamily superfamily	a.260.1 — Rhabdovirus nucleoprotein-like
Family Family family	a.260.1.1 — Rhabdovirus nucleocapsid protein

CATH v4.4 (10 domains)

Domain ID domain_id	3ptoA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
Homologous superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

Domain ID domain_id	3ptoA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3610 — Rhabdovirus nucleoprotein-like
Homologous superfamily homologous superfamily	10 — Nucleoprotein

Domain ID domain_id	3ptoB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
Homologous superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

Domain ID domain_id	3ptoB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3610 — Rhabdovirus nucleoprotein-like
Homologous superfamily homologous superfamily	10 — Nucleoprotein

Domain ID domain_id	3ptoC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
Homologous superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

Domain ID domain_id	3ptoC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3610 — Rhabdovirus nucleoprotein-like
Homologous superfamily homologous superfamily	10 — Nucleoprotein

Domain ID domain_id	3ptoD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
Homologous superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

Domain ID domain_id	3ptoD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3610 — Rhabdovirus nucleoprotein-like
Homologous superfamily homologous superfamily	10 — Nucleoprotein

Domain ID domain_id	3ptoE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3570 — Rhabdovirus nucleoprotein-like fold
Homologous superfamily homologous superfamily	10 — Rhabdovirus nucleocapsid protein like domain

Domain ID domain_id	3ptoE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3610 — Rhabdovirus nucleoprotein-like
Homologous superfamily homologous superfamily	10 — Nucleoprotein

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Unit-cell length a length_a	165.643 Å
Unit-cell length b length_b	234.062 Å
Unit-cell length c length_c	75.975 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	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.008 Å
Low-resolution limit resolution_low	38.763 Å
R factor r_factor	0.2592
R_work r_work	0.2579
R_free r_free	0.2907

Crystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex

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

Nucleoprotein

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

3pto__assembly_1__model_1

3pto__assembly_1__model_1 | I(q)

3pto__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex

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

Nucleoprotein

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

3pto__assembly_1__model_1

3pto__assembly_1__model_1 | I(q)

3pto__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)