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- EMDB-71804: Linear arrangement of the HDV 311-RNP -

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Basic information

Entry
Database: EMDB / ID: EMD-71804
TitleLinear arrangement of the HDV 311-RNP
Map dataLinear arrangement of 311-RNP. Unsharpened.
Sample
  • Complex: Linear arrangement map of S-HDAg bound to 311-agRNA
    • Complex: S-HDAg
      • Protein or peptide: HDV delta antigen, HDAg
    • Complex: 311-agRNA
      • RNA: Truncated HDV antigenomic RNA, 311-agRNA
KeywordsHDV / HDAg / RNP / RNA / VIRUS
Function / homology
Function and homology information


virion component / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / RNA binding
Similarity search - Function
Hepatitis delta virus delta antigen / Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile.
Similarity search - Domain/homology
Biological speciesHepatitis delta virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 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_71804.png

Downloads & links

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Map

FileDownload / File: emd_71804.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLinear arrangement of 311-RNP. Unsharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.52 Å/pix.
x 300 pix.
= 455. Å		1.52 Å/pix.
x 300 pix.
= 455. Å		1.52 Å/pix.
x 300 pix.
= 455. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.51667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0738
Minimum - Maximum-0.16575871 - 0.39365497
Average (Standard dev.)-0.0003790258 (±0.013136204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 455.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Linear arrangement of 311-RNP. Half map - A.

Fileemd_71804_half_map_1.map
AnnotationLinear arrangement of 311-RNP. Half map - A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Linear arrangement of 311-RNP. Half map - B.

Fileemd_71804_half_map_2.map
AnnotationLinear arrangement of 311-RNP. Half map - B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Linear arrangement map of S-HDAg bound to 311-agRNA

EntireName: Linear arrangement map of S-HDAg bound to 311-agRNA
Components
  • Complex: Linear arrangement map of S-HDAg bound to 311-agRNA
    • Complex: S-HDAg
      • Protein or peptide: HDV delta antigen, HDAg
    • Complex: 311-agRNA
      • RNA: Truncated HDV antigenomic RNA, 311-agRNA

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Supramolecule #1: Linear arrangement map of S-HDAg bound to 311-agRNA

SupramoleculeName: Linear arrangement map of S-HDAg bound to 311-agRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: S-HDAg

SupramoleculeName: S-HDAg / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Hepatitis delta virus

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Supramolecule #3: 311-agRNA

SupramoleculeName: 311-agRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Hepatitis delta virus / Synthetically produced: Yes

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Macromolecule #1: HDV delta antigen, HDAg

MacromoleculeName: HDV delta antigen, HDAg / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis delta virus
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SRPEGRKNRG GREEVLEQWV SGRKKLEELE RDLRKVKKKI KKLEDEHPWL GNIKGILGKK DKDGEGAPPA KRARTDQMEV DSGPRKRPSR GGFTDKERQD HRRRKALENK RKQLSAGGKN LSKEEEEELR RLTEEDERRE RRIAGPQVGG VNPLEGGTRG APGGGFVPSM ...String:
SRPEGRKNRG GREEVLEQWV SGRKKLEELE RDLRKVKKKI KKLEDEHPWL GNIKGILGKK DKDGEGAPPA KRARTDQMEV DSGPRKRPSR GGFTDKERQD HRRRKALENK RKQLSAGGKN LSKEEEEELR RLTEEDERRE RRIAGPQVGG VNPLEGGTRG APGGGFVPSM QGVPESPFTR TGEGLDIRGS QGFP

UniProtKB: Small delta antigen

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Macromolecule #2: Truncated HDV antigenomic RNA, 311-agRNA

MacromoleculeName: Truncated HDV antigenomic RNA, 311-agRNA / type: rna / ID: 2
Details: 311 nucleotides derived from HDV antigenomic RNA. Residues from the T7 promoter (GGGAGA) and EcoRI restriction site (AAGCU) are added to start and end of sequence, respectively.
Source (natural)Organism: Hepatitis delta virus
SequenceString: GGGAGAUUUU UCCUUCUUGG GAGUUGUAUC UCCGACGUUC CAAUGCUCUU UACCGACUCA CCCCUCUCGG GCGCUGAUCU AUCCUCCCCG CGAAUCCUUG UUCGGAACUU GGCUCAUCUC GAACUUGGGC GACAGGGCCA GCAGUCUCCU CUUUACAGAA AAGAGUAAGA ...String:
GGGAGAUUUU UCCUUCUUGG GAGUUGUAUC UCCGACGUUC CAAUGCUCUU UACCGACUCA CCCCUCUCGG GCGCUGAUCU AUCCUCCCCG CGAAUCCUUG UUCGGAACUU GGCUCAUCUC GAACUUGGGC GACAGGGCCA GCAGUCUCCU CUUUACAGAA AAGAGUAAGA GUACUGAGGA CCGUCGCCUC UAGUCGAAGA UGAGCCGGCC CGAAGGAAGG AAAAACCGCG GGGGGAGAGA AGAGGUUCUC GAGCAGUGGG UGAGCGGAAG AAAGAAGUUA GAGGAACUCG AGAGAGACCU CCGGAAGGUU AAGAAGAAAG CU

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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
Component:
ConcentrationNameFormula
20.0 mMTris(hydroxymethyl)aminomethane hydrochloride
200.0 mMsodium chlorideNaCl

Details: 20mM Tris-HCl, 200mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.72 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 552252 / Details: Topaz (tbepler) particle picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Details: Non-uniform refinement from CryoSPARC / Number images used: 37594
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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