SAXSdb — 1wcd

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

MAJOR STRUCTURAL PROTEIN VP2

INFECTIOUS BURSAL DISEASE VIRUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	water × 60	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 20	water × 20	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_IBDVC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain J； PDBConstruct 1–441； UniProt 1–441

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	1wcd
Deposition date deposition_date	2004-11-12
Structure title title	Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution
Keywords keywords	;VIRUS, NON-ENVELOPED ICOSAHEDRAL VIRUSES, DOUBLE-STRANDED RNA VIRUS PROTEIN, BIRNAVIRUS, TRANSCRIPTASE MACHINERY, HYDROLASE, MEMBRANE TRANSLOCATION ACTIVITY, EVOLUTION, ICOSAHEDRAL 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.

1wcd__assembly_1__model_1

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

Download this curve (.dat)

1wcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	93.24 Å
Rg (electron density)	91.68 Å
Total Rg	91.80 Å
Atom count	190140
Residues	25260
Excluded volume	3394000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wcd__assembly_1__model_1`	60-MERIC （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wcd__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1wcd__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1wcd__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1wcd__assembly_5__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1wcd__assembly_6__model_1`	eicosameric （20）	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	MAJOR STRUCTURAL PROTEIN VP2
Molecular weight formula_weight	47192.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J
Atom count atom_count	3206

MTNLQDQTQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVADLNSPLKIAGA

Source Source

Source organism organism	INFECTIOUS BURSAL DISEASE VIRUS
Common name common_name	IBDV
NCBI taxonomy ID ncbi_taxonomy_id	10995
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wcdj1
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.121.4.9 — Birnaviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id	1wcdJ01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1wcdJ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	660 — icosahedral virus

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Unit-cell length a length_a	258.929 Å
Unit-cell length b length_b	258.929 Å
Unit-cell length c length_c	347.186 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2490

Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution

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

MAJOR STRUCTURAL PROTEIN VP2

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

1wcd__assembly_1__model_1

1wcd__assembly_1__model_1 | I(q)

1wcd__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution

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

MAJOR STRUCTURAL PROTEIN VP2

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

1wcd__assembly_1__model_1

1wcd__assembly_1__model_1 | I(q)

1wcd__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)