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6bvn

Cryo-EM Structure of Hepatitis B virus T=3 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein

Hepatitis B virus genotype D subtype adw

UniProt P03147

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 180 Heteroaryldihydropyrimidine tetramethylrodamine × 60 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 3 Heteroaryldihydropyrimidine tetramethylrodamine × 1 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 15 Heteroaryldihydropyrimidine tetramethylrodamine × 5 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 18 Heteroaryldihydropyrimidine tetramethylrodamine × 6 Consistent with protein count
5 Protein homooligomer Homooligomer Protein 3 Heteroaryldihydropyrimidine tetramethylrodamine × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3kxs 3kxs 3kxs 4bmg 4bmg 4bmg 7k5m 7k5m 7k5m 9n3h

10 assemblies

Homotetramer
2g33 2g33 2g34 2g34 2qij 2qij 4g93 4g93 5d7y 5d7y 6bvf 6bvf

18 assemblies; showing the first 12

Other homooligomers
2g33 2g33 2g33 2g33 2g34 2g34 2g34 2g34 2qij 2qij 2qij 2qij

43 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
6cwd 6cwd 6cwt

3 assemblies

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

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_id6bvn
Deposition date deposition_date2017-12-13
Structure title titleCryo-EM Structure of Hepatitis B virus T=3 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA
Keywords keywordscapsid, CpAM, antiviral, fluorescent, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
Experimental Method methodELECTRON MICROSCOPY
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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.

6bvn__assembly_1__model_1

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

Download this curve (.dat)

6bvn__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6bvn__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）0.00 Å
Rg (electron density)127.90 Å
Total Rg128.10 Å
Atom count211020
Residues25920
Excluded volume3762500 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6bvn__assembly_1__model_1 180-meric （180） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6bvn__assembly_2__model_1 trimeric （3） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 6bvn__assembly_3__model_1 pentadecameric （15） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 6bvn__assembly_4__model_1 octadecameric （18） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 6bvn__assembly_5__model_1 trimeric （3） 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)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6bvnA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily10 — Viral capsid, core domain supefamily, Hepatitis B virus
Domain ID domain_id6bvnB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily10 — Viral capsid, core domain supefamily, Hepatitis B virus
Domain ID domain_id6bvnC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology4090 — Hepatitis B viral capsid (hbcag) fold
Homologous superfamily homologous superfamily10 — Viral capsid, core domain supefamily, Hepatitis B virus
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7. Citations (1)