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- EMDB-71803: HDV particle subtomogram reconstruction -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71803
TitleHDV particle subtomogram reconstruction
Map dataHDV particle subtomogram reconstruction. Unsharpened.
Sample
  • Virus: Hepatitis delta virus
KeywordsHDV / HDAg / RNP / cryo-ET / VIRUS
Biological speciesHepatitis delta virus
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 Å
AuthorsItskanov S / Lansdon EB
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Structural characterization of the HDV virion and its ribonucleoprotein
Authors: Itskanov S / Ary B / Mehra U / Lew I / Novikov N / Schmitz U / Holdorf MM / Beran RK / Lansdon EB
History
DepositionJul 23, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71803.png

Downloads & links

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Map

FileDownload / File: emd_71803.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHDV particle subtomogram reconstruction. Unsharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 474.624 Å		0.93 Å/pix.
x 512 pix.
= 474.624 Å		0.93 Å/pix.
x 512 pix.
= 474.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.927 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.81
Minimum - Maximum-9.663264 - 8.652202000000001
Average (Standard dev.)0.11088438 (±0.99997455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin276276276
Dimensions512512512
Spacing512512512
CellA=B=C: 474.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HDV particle subtomogram reconstruction. Half map - even.

Fileemd_71803_half_map_1.map
AnnotationHDV particle subtomogram reconstruction. Half map - even.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HDV particle subtomogram reconstruction. Half map - odd.

Fileemd_71803_half_map_2.map
AnnotationHDV particle subtomogram reconstruction. Half map - odd.
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 delta virus

EntireName: Hepatitis delta virus
Components
  • Virus: Hepatitis delta virus

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Supramolecule #1: Hepatitis delta virus

SupramoleculeName: Hepatitis delta virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12475 / Sci species name: Hepatitis delta virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 350.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 25mM Tris-HCl pH 8.0, 150mM NaCl, 1mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 358
ExtractionNumber tomograms: 912 / Number images used: 358 / Software - Name: EMAN2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
FSC plot (resolution estimation)

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