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- EMDB-73226: HBV wildtype capsid with packaged E. coli RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-73226
TitleHBV wildtype capsid with packaged E. coli RNA
Map dataHBV WT capsid with packaged E. coli RNA. I2 symmetry imposed.
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: 3.9 Å
AuthorsGibes NG / Wang JC-Y / Zlotnick A / Kumar S
Funding support United States, 2 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
CitationJournal: Sci Adv / Year: 2026
Title: Negative cooperativity drives activity of capsid-directed antivirals against hepatitis B virus.
Authors: Caleb J Valkner / Nora Gibes / Marina Sicheng Xie / Smita Nair / Shiv Kumar / Samson Francis / Balasubramanian Venkatakrishnan / Irina Tsvetkova / Angela Patterson / Michael VanNieuwenhze / ...Authors: Caleb J Valkner / Nora Gibes / Marina Sicheng Xie / Smita Nair / Shiv Kumar / Samson Francis / Balasubramanian Venkatakrishnan / Irina Tsvetkova / Angela Patterson / Michael VanNieuwenhze / Bogdan Dragnea / Joseph Che-Yen Wang / Adam Zlotnick /
Abstract: Hepatitis B virus capsid protein plays a role in almost every step of viral replication, from self-assembly to genome release. This makes capsid protein an attractive target for antiviral development. ...Hepatitis B virus capsid protein plays a role in almost every step of viral replication, from self-assembly to genome release. This makes capsid protein an attractive target for antiviral development. Capsid assembly modulators (CAMs) are direct-acting antivirals that bind capsid protein, leading to empty or aberrant complexes instead of an infectious virus. CAMs can also disrupt the capsid, preventing new infection. To understand CAM activity, we examined the energetics of CAM-capsid interaction. We observed negative cooperativity of CAM-binding kinetics and thermodynamics. These correlate with large changes in capsid architecture that presage capsid rupture. We propose that CAMs induce an accumulated strain on the capsid. Understanding the interplay of forces and architecture will help guide the development of CAMs.
History
DepositionOct 11, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73226.png

Downloads & links

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Map

FileDownload / File: emd_73226.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHBV WT capsid with packaged E. coli RNA. I2 symmetry imposed.
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: 0.0131
Minimum - Maximum-0.04223727 - 0.06794242
Average (Standard dev.)0.00014773286 (±0.004211559)
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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Half map: #1

Fileemd_73226_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_73226_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 : 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 / Details: HBV capsid protein / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYVN TNMGLKFRQL LWFHISCLTF GRETVIEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRGRSPRRRT PSPRRRRSQS PRRRRSQSRE SQC

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / 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

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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: 232804
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1), RELION (ver. 3.1.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: RELION SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 42786
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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