4bmg

Crystal structure of hexameric HBc149 Y132A

Method: X-RAY DIFFRACTION

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

CAPSID PROTEIN

HEPATITIS B VIRUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAPSD_HBVD1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149 Author chain D； PDBConstruct 1–149； UniProt 1–149 Author chain E； PDBConstruct 1–149； UniProt 1–149 Author chain F； PDBConstruct 1–149； UniProt 1–149

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	4bmg
Deposition date deposition_date	2013-05-08
Structure title title	Crystal structure of hexameric HBc149 Y132A
Keywords keywords	VIRAL PROTEIN, PROTEIN FOLDING, ALLOSTERY; 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.

4bmg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4bmg__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bmg__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	21.79 Å
Rg (electron density)	21.03 Å
Total Rg	21.74 Å
Atom count	2258
Residues	285
Excluded volume	40433 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bmg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4bmg__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4bmg__assembly_3__model_1`	dimeric （2）	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 (1)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4bmga_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d4bmgb_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d4bmgc_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d4bmgd_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d4bmge_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

Domain ID domain_id	d4bmgf_
Class class	a — All alpha proteins
Fold Fold fold	a.62 — Hepatitis B viral capsid (hbcag)
Superfamily Superfamily superfamily	a.62.1 — Hepatitis B viral capsid (hbcag)
Family Family family	a.62.1.1 — Hepatitis B viral capsid (hbcag)

CATH v4.4 (6 domains)

Domain ID domain_id	4bmgA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	4bmgB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	4bmgC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	4bmgD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	4bmgE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

Domain ID domain_id	4bmgF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily	10 — Viral capsid, core domain supefamily, Hepatitis B virus

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Unit-cell length a length_a	64.790 Å
Unit-cell length b length_b	67.750 Å
Unit-cell length c length_c	86.610 Å
Unit-cell angle α angle_alpha	68.98 °
Unit-cell angle β angle_beta	70.75 °
Unit-cell angle γ angle_gamma	84.51 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	44.526 Å
R factor r_factor	0.2555
R_work r_work	0.2521
R_free r_free	0.3173

Description description	CAPSID PROTEIN
Molecular weight formula_weight	17358.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6775

Crystal structure of hexameric HBc149 Y132A

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

CAPSID PROTEIN

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

4bmg__assembly_3__model_1

4bmg__assembly_3__model_1 | I(q)

4bmg__assembly_3__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	HEPATITIS B VIRUS
NCBI taxonomy ID ncbi_taxonomy_id	10407
Host organism host_organism	ESCHERICHIA COLI

Crystal structure of hexameric HBc149 Y132A

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

CAPSID PROTEIN

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

4bmg__assembly_3__model_1

4bmg__assembly_3__model_1 | I(q)

4bmg__assembly_3__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)