SAXSdb — 1nov

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

NODAMURA VIRUS COAT PROTEINS

Nodamura virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 360	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 30	No other associated polymer	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 36	No other associated polymer	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 720	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COAT_NODAV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain B； PDBConstruct 1–355； UniProt 1–355 Author chain C； PDBConstruct 1–355； UniProt 1–355 Author chain D； PDBConstruct 1–44； UniProt 356–399 Author chain E； PDBConstruct 1–44； UniProt 356–399 Author chain F； PDBConstruct 1–44； UniProt 356–399

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	1nov
Deposition date deposition_date	1997-09-16
Structure title title	NODAMURA VIRUS
Keywords keywords	INSECT VIRUS, NODAMURA VIRUS, COAT PROTEIN, Icosahedral virus, Virus; VIRUS
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.

1nov__assembly_1__model_1

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

Download this curve (.dat)

1nov__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nov__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)	139.10 Å
Total Rg	139.20 Å
Atom count	447060
Residues	59760
Excluded volume	7971400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nov__assembly_1__model_1`	360-MERIC （360）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nov__assembly_2__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1nov__assembly_3__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1nov__assembly_4__model_1`	36-meric （36）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1nov__assembly_5__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1nov__assembly_6__model_1`	720-MERIC （720）	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 (2)

Entity 1 Entity 1 polymer

Description description	NODAMURA VIRUS COAT PROTEINS
Molecular weight formula_weight	38508.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7451

MVSKAARRRRAAPRQQQRQQSNRASNQPRRRRARRTRRQQRMAATNNMLKMSAPGLDFLKCAFASPDFSTDPGKGIPDKFQGLVLPKKHCLTQSITFTPGKQTMLLVAPIPGIACLKAEANVGASFSGVPLASVEFPGFDQLFGTSATDTAANVTAFRYASMAAGVYPTSNLMQFAGSIQVYKIPLKQVLNSYSQTVATVPPTNLAQNTIAIDGLEALDALPNNNYSGSFIEGCYSQSVCNEPEFEFHPIMEGYASVPPANVTNAQASMFTNLTFSGARYTGLGDMDAIAILVTTPTGAVNTAVLKVWACVEYRPNPNSTLYEFARESPANDEYALAAYRKIARDIPIAVACKDN

Source Source

Source organism organism	Nodamura virus
NCBI taxonomy ID ncbi_taxonomy_id	12288
Host organism host_organism	Galleria mellonella

Entity 2 Entity 2 polymer

Description description	NODAMURA VIRUS COAT PROTEINS
Molecular weight formula_weight	4618.4 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

ATFWERVRSILKSGLNFASTIPGPVGVAATGIKGIIETIGSLWV

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nova_
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	d1novb_
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	d1novc_
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	1novA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1novB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1novC00
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	562.090 Å
Unit-cell length b length_b	354.130 Å
Unit-cell length c length_c	612.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	720

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2960
R_work r_work	0.2960
R_free r_free	—

NODAMURA VIRUS

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

NODAMURA VIRUS COAT PROTEINS

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

1nov__assembly_1__model_1

1nov__assembly_1__model_1 | I(q)

1nov__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 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (5)

NODAMURA VIRUS

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

NODAMURA VIRUS COAT PROTEINS

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

1nov__assembly_1__model_1

1nov__assembly_1__model_1 | I(q)

1nov__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 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (5)