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- EMDB-18000: Hepatitis B core protein with bound P1dC -

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Basic information

Entry
Database: EMDB / ID: EMD-18000
TitleHepatitis B core protein with bound P1dC
Map data
Sample
  • Virus: Hepatitis B virus
    • Protein or peptide: External core antigen
    • Protein or peptide: P1dC
KeywordsHepatitis B core protein / Spikes dimeric peptide binder aggregator Hepatitis B virus Capsid LIKE PARTICLE / VIRUS LIKE PARTICLE
Function / homologyHepatitis 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 / structural molecule activity / extracellular region / External core antigen
Function and homology information
Biological speciesHepatitis B virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMakbul C / Khayenko V / Maric MH / Bottcher B
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)BO1150/17-1 Germany
German Research Foundation (DFG)MA6957/1-1 Germany
German Research Foundation (DFG)INST 93/903-1 Germany
German Research Foundation (DFG)INST 93/1042-1 Germany
German Research Foundation (DFG)INST 93/1143-1 Germany
CitationJournal: Elife / Year: 2025
Title: Induction of hepatitis B core protein aggregation targeting an unconventional binding site
Authors: Khayenko V / Makbul C / Schulte C / Hemmelmann N / Kachler S / Bottcher B / Maric HM / Comas-Garcia M / Dotsch V
History
DepositionJul 22, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18000.png

Downloads & links

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Map

FileDownload / File: emd_18000.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 467.94 Å		1.06 Å/pix.
x 440 pix.
= 467.94 Å		1.06 Å/pix.
x 440 pix.
= 467.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.2207165 - 2.7018368
Average (Standard dev.)0.0056232056 (±0.21139279)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 467.94003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18000_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18000_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Hepatitis B virus

EntireName: Hepatitis B virus
Components
  • Virus: Hepatitis B virus
    • Protein or peptide: External core antigen
    • Protein or peptide: P1dC

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Sci species strain: ayw/France/Tiollais/1979 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5 MDa
Virus shellShell ID: 1 / Diameter: 360.0 Å / T number (triangulation number): 4

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Macromolecule #1: External core antigen

MacromoleculeName: External core antigen / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 21.146217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV RRRGRSPRRR T PSPRRRRS QSPRRRRSQS RESQC

UniProtKB: External core antigen

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Macromolecule #2: P1dC

MacromoleculeName: P1dC / type: protein_or_peptide / ID: 2
Details: The binder consists of 2 peptide moieties linked by a PEG-linker: The peptide moiety is 'MHRSLLGRMKGA' The resolved density has a length of 6 residues of the moiety. The position is ...Details: The binder consists of 2 peptide moieties linked by a PEG-linker: The peptide moiety is 'MHRSLLGRMKGA' The resolved density has a length of 6 residues of the moiety. The position is unresolved and modelled as Poly-Ala
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.039273 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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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

Concentration4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2784 / Average exposure time: 2.5 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 75000
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: 36817 / Details: template picked
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: unpublished map of related sample
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Software - details: none uniform refinement / Number images used: 22830
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7od4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8px3:
Hepatitis B core protein with bound P1dC

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