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- EMDB-29858: Hepatitis B virus capsid bound to importin alpha1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29858
TitleHepatitis B virus capsid bound to importin alpha1
Map data
Sample
  • Complex: Capsid formed by Cp183 when importin alpha1 is incorporated
    • Protein or peptide: Core protein Cp183
KeywordsCapsid formed by Cp183 when bound to importin alpha1 / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang R / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of Hepatitis B virus capsid bound to importin alpha1
Authors: Yang R / Cingolani G
History
DepositionFeb 20, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29858.png

Downloads & links

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Map

FileDownload / File: emd_29858.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.108 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03192083 - 0.084303856
Average (Standard dev.)0.00096620974 (±0.0043954765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 531.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29858_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29858_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Capsid formed by Cp183 when importin alpha1 is incorporated

EntireName: Capsid formed by Cp183 when importin alpha1 is incorporated
Components
  • Complex: Capsid formed by Cp183 when importin alpha1 is incorporated
    • Protein or peptide: Core protein Cp183

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Supramolecule #1: Capsid formed by Cp183 when importin alpha1 is incorporated

SupramoleculeName: Capsid formed by Cp183 when importin alpha1 is incorporated
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus

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Macromolecule #1: Core protein Cp183

MacromoleculeName: Core protein Cp183 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 16.328719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLP

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qgt

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37698
FSC plot (resolution estimation)

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