3hhw

Complex of a vesicular stomatitis virus empty capsid with 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 heterocomplex	Heteromer	Protein 20	Nucleoprotein × 10 （Q77E03） D(-)-TARTARIC ACID × 12	Consistent with protein count

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 heterocomplex	Heteromer	Protein 20	Phosphoprotein × 10 （P04880） D(-)-TARTARIC ACID × 12	Consistent with protein count

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	3hhw
Deposition date deposition_date	2009-05-18
Structure title title	Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein
Keywords keywords	;protein complex, template, replication, negative strand RNA virus, Chaperone, Phosphoprotein, RNA replication, Virion, Ribonucleoprotein, RNA-binding, Viral nucleoprotein, 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.

3hhw__assembly_1__model_1

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

Download this curve (.dat)

3hhw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hhw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.75 Å
Rg (electron density)	59.06 Å
Total Rg	59.31 Å
Atom count	39230
Residues	4920
Excluded volume	700900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hhw__assembly_1__model_1`	eicosameric （20）	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	9887.0 kDa
Mutation mutation	S290W
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	19615

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	47431.9 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

SVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGLTNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYWSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRAVMSLQGLREKTIGKYAKSEFDK

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 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3hhwk_
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	d3hhwl_
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	d3hhwm_
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	d3hhwn_
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	d3hhwo_
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 (15 domains)

Domain ID domain_id	3hhwA00
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	3hhwB00
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	3hhwC00
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	3hhwD00
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	3hhwE00
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	3hhwK01
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	3hhwK02
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	3hhwL01
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	3hhwL02
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	3hhwM01
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	3hhwM02
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	3hhwN01
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	3hhwN02
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	3hhwO01
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	3hhwO02
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	170.602 Å
Unit-cell length b length_b	234.520 Å
Unit-cell length c length_c	95.050 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	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2645
R_work r_work	0.2629
R_free r_free	0.2957

Complex of a vesicular stomatitis virus empty capsid with 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

3hhw__assembly_1__model_1

3hhw__assembly_1__model_1 | I(q)

3hhw__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Complex of a vesicular stomatitis virus empty capsid with 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

3hhw__assembly_1__model_1

3hhw__assembly_1__model_1 | I(q)

3hhw__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

CATH v4.4 (15 domains)

7. Citations (1)