3hhz

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein

Method: X-RAY DIFFRACTION

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

Phosphoprotein

Vesicular stomatitis Indiana virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	Nucleoprotein × 10 （Q77E03） RNA (45-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHOSP_VSIVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–87； UniProt 183–265 Author chain B； PDBConstruct 5–87； UniProt 183–265 Author chain C； PDBConstruct 5–87； UniProt 183–265 Author chain D； PDBConstruct 5–87； UniProt 183–265 Author chain E； PDBConstruct 5–87； UniProt 183–265

Nucleoprotein

Vesicular stomatitis Indiana virus

UniProt Q77E03

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	Phosphoprotein × 10 （P04880） RNA (45-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCAP_VSIVN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–421； UniProt 2–422 Author chain L； PDBConstruct 1–421； UniProt 2–422 Author chain M； PDBConstruct 1–421； UniProt 2–422 Author chain N； PDBConstruct 1–421； UniProt 2–422 Author chain O； 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	3hhz
Deposition date deposition_date	2009-05-18
Structure title title	Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein
Keywords keywords	;Protein, RNA, template, replication, negative strand RNA virus, Chaperone, Phosphoprotein, RNA replication, Virion, Ribonucleoprotein, RNA-binding, Viral nucleoprotein, VIRAL PROTEIN, 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.

3hhz__assembly_1__model_1

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

Download this curve (.dat)

3hhz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hhz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.95 Å
Rg (electron density)	58.64 Å
Total Rg	58.79 Å
Atom count	40830
Residues	5030
Excluded volume	723750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hhz__assembly_1__model_1`	22-meric （22）	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	Phosphoprotein
Molecular weight formula_weight	9793.2 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	20415

GSHMVMNTHPYQSEAVSDVWSLSKTSMTFQPKKASLQPLTISLDELFSSRGEFISVGGNGRMSHKEAILLGLRYKKLYNQARVKYSL

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	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	K,L,M,N,O

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 3 Entity 3 polymer

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

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	3hhzA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	440 — Vesicular stomatitis virus phosphoprotein C-terminal domain

Domain ID domain_id	3hhzB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	440 — Vesicular stomatitis virus phosphoprotein C-terminal domain

Domain ID domain_id	3hhzC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	440 — Vesicular stomatitis virus phosphoprotein C-terminal domain

Domain ID domain_id	3hhzD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	440 — Vesicular stomatitis virus phosphoprotein C-terminal domain

Domain ID domain_id	3hhzE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	440 — Vesicular stomatitis virus phosphoprotein C-terminal domain

Domain ID domain_id	3hhzK01
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	3hhzK02
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	3hhzL01
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	3hhzL02
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	3hhzM01
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	3hhzM02
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	3hhzN01
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	3hhzN02
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	3hhzO01
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	3hhzO02
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	166.568 Å
Unit-cell length b length_b	235.248 Å
Unit-cell length c length_c	96.138 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	3.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2579
R_work r_work	0.2542
R_free r_free	0.3233

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein

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

Phosphoprotein

State in the Current Structure

Other States of the Same Protein in the Database

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

3hhz__assembly_1__model_1

3hhz__assembly_1__model_1 | I(q)

3hhz__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein

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

Phosphoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

3hhz__assembly_1__model_1

3hhz__assembly_1__model_1 | I(q)

3hhz__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)