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- EMDB-73227: Focused map of HBV with BAY41-4109 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73227
TitleFocused map of HBV with BAY41-4109
Map dataFocused map of empty HBV with BAY41-4109
Sample
  • Virus: Hepatitis B virus subtype adyw
    • Protein or peptide: Capsid protein
KeywordsHBV / CAM / VIRUS
Biological speciesHepatitis B virus / Hepatitis B virus subtype adyw
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsGibes NG / Wang JC-Y / Zlotnick A / Kumar S
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118933 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144022 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI173104 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI043453 United States
CitationJournal: To Be Published
Title: Negative cooperativity drives activity of capsid-directed antivirals against Hepatitis B Virus
Authors: Valkner CJ / Gibes NG / Xie MS / Kumar S / Francis S / Venkatakrishnan B / Tsvetkova I / Patterson A / VanNieuwenhze M / Dragnea B / Wang JC-Y / Zlotnick A
History
DepositionOct 12, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73227.png

Downloads & links

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Map

FileDownload / File: emd_73227.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of empty HBV with BAY41-4109
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å		1.4 Å/pix.
x 320 pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0088
Minimum - Maximum-0.07014792 - 0.093617305
Average (Standard dev.)0.000012273174 (±0.0017642964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73227_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Odd map

Fileemd_73227_half_map_1.map
AnnotationOdd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even map

Fileemd_73227_half_map_2.map
AnnotationEven 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 : Hepatitis B virus subtype adyw

EntireName: Hepatitis B virus subtype adyw
Components
  • Virus: Hepatitis B virus subtype adyw
    • Protein or peptide: Capsid protein

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Supramolecule #1: Hepatitis B virus subtype adyw

SupramoleculeName: Hepatitis B virus subtype adyw / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinant full length HBV capsid protein expressed in E. coli.
NCBI-ID: 10419 / Sci species name: Hepatitis B virus subtype adyw / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid protein / Diameter: 340.0 Å / T number (triangulation number): 4

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYVN TNMGLKFRQL LWFHISCLTF GRETVIEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRG

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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: 7.5 / Details: 30mM NaCl, 50mM Tris-HCl(pH7.5), 2mM DTT
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 28.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67538 / Details: Particle number before symmetry expansion
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.4), RELION (ver. 3.1.3)) / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: RELION SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Details: Particle number after symmetry expansion / Number images used: 457684
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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