SAXSdb — 3pu4

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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–RNA	Homooligomer	Protein 10 RNA 2	RNA (45-MER) × 2 URANYL (VI) ION × 40	Consistent with all polymers

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	3pu4
Deposition date deposition_date	2010-12-03
Structure title title	Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyU complex
Keywords keywords	RNA, nucleocapsid, VIRAL PROTEIN-RNA complex; VIRAL PROTEIN/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.

3pu4__assembly_1__model_1

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

Download this curve (.dat)

3pu4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pu4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	57.63 Å
Rg (electron density)	57.55 Å
Total Rg	57.58 Å
Atom count	34874
Residues	4262
Excluded volume	618220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pu4__assembly_1__model_1`	dodecameric （12）	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 (3)

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	17437

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 polymer

Description description	RNA (45-MER)
Molecular weight formula_weight	13732.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

Entity 3 Entity 3 non-polymer

Description description	URANYL (VI) ION
Molecular weight formula_weight	270.0 kDa
Source method src_method	syn
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3pu4A01
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	3pu4A02
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	3pu4B01
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	3pu4B02
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	3pu4C01
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	3pu4C02
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	3pu4D01
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	3pu4D02
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	3pu4E01
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	3pu4E02
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	165.477 Å
Unit-cell length b length_b	235.065 Å
Unit-cell length c length_c	75.498 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	3.000 Å
Low-resolution limit resolution_low	34.774 Å
R factor r_factor	0.2519
R_work r_work	0.2506
R_free r_free	0.2883

Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyU 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

3pu4__assembly_1__model_1

3pu4__assembly_1__model_1 | I(q)

3pu4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyU 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

3pu4__assembly_1__model_1

3pu4__assembly_1__model_1 | I(q)

3pu4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)