SAXSdb — 3fbm

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

Polyprotein

Avian 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	CALCIUM ION × 60	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	CALCIUM ION × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	CALCIUM ION × 6	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 60	CALCIUM ION × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WI42_IBDV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 1–452

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	3fbm
Deposition date deposition_date	2008-11-19
Structure title title	D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles
Keywords keywords	capsid protein, autoproteolytic activity, capsid maturation, virus assembly, IBDV, 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.

3fbm__assembly_1__model_1

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

Download this curve (.dat)

3fbm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fbm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	92.65 Å
Rg (electron density)	91.08 Å
Total Rg	91.16 Å
Atom count	192600
Residues	25680
Excluded volume	3442000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fbm__assembly_1__model_1`	60-MERIC （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fbm__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3fbm__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3fbm__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3fbm__assembly_5__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`3fbm__assembly_6__model_1`	60-meric （60）	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	Polyprotein
Molecular weight formula_weight	48470.7 kDa
Mutation mutation	D431N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3210

MTNLSDQTQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVANLNSPLKIAGAFGFKDIIRAIR

Source Source

Source organism organism	Avian Infectious bursal disease virus
Common name common_name	IBDV
NCBI taxonomy ID ncbi_taxonomy_id	10995
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3fbma_
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	3fbmA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3fbmA02
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	326.725 Å
Unit-cell length b length_b	326.725 Å
Unit-cell length c length_c	326.725 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	240

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2940
R_work r_work	0.2940
R_free r_free	0.2910

D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles

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

Polyprotein

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

3fbm__assembly_1__model_1

3fbm__assembly_1__model_1 | I(q)

3fbm__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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles

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

Polyprotein

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

3fbm__assembly_1__model_1

3fbm__assembly_1__model_1 | I(q)

3fbm__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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)