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- EMDB-71807: HDAg complex with 86-pRNA, Body1 -

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Basic information

Entry
Database: EMDB / ID: EMD-71807
TitleHDAg complex with 86-pRNA, Body1
Map dataBody 1 of 86-pRNP (HDAg 86-pRNA). Unsharpened
Sample
  • Complex: Complex of S-HDAg bound to 86-pRNA
    • Complex: S-HDAg
      • Protein or peptide: Small delta antigen
    • Complex: 86-pRNA
      • RNA: Palindromic RNA
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 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsItskanov S / Lansdon EB
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural characterization of the HDV virion and its ribonucleoprotein.
Authors: Samuel Itskanov / Beatrice Ary / Upasana Mehra / Irene Lew / Nikolai Novikov / Uli Schmitz / Meghan M Holdorf / Rudolf K Beran / Eric B Lansdon /
Abstract: Hepatitis D virus (HDV) is a small RNA satellite virus of hepatitis B virus (HBV) which encodes a single protein, HDV delta antigen (HDAg), that is required for replication. Viral replication occurs ...Hepatitis D virus (HDV) is a small RNA satellite virus of hepatitis B virus (HBV) which encodes a single protein, HDV delta antigen (HDAg), that is required for replication. Viral replication occurs independently from HBV and relies primarily on host RNA polymerase(s). Bulevirtide, a viral entry inhibitor, is the only approved treatment for chronic HDV but has a low cure rate as a monotherapy, and most patients rebound following cessation of therapy. It is likely that an inhibitor targeting HDV replication is necessary to achieve HDV cure, but the paucity of HDV-derived elements and limited understanding of HDV replication presents a significant therapeutic challenge. Understanding the precise mechanism of interactions between HDAg and viral RNA, and how it is packaged within the virion can inspire structure-guided drug design targeting replication. Using cryoelectron tomography and single particle cryoelectron microscopy, we present reconstructions of the virion and viral RNPs. We observed multiple binding configurations in vitro that suggest a propensity to arrange four RNA segments around repeating units of HDAg in a ladder-like formation. The oligomerization domains of a homo-octameric HDAg complex are directly involved in RNA binding by utilizing the vertices and sides of its square-shaped architecture to bind RNA in a sequence-promiscuous fashion. Structure-function analysis reveals that these RNA contact sites are important for viral replication and their disruption may be a potential avenue for next-generation antivirals to treat HDV.
History
DepositionJul 23, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71807.png

Downloads & links

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Map

FileDownload / File: emd_71807.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody 1 of 86-pRNP (HDAg 86-pRNA). Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00115
Minimum - Maximum-0.006331837 - 0.012377339
Average (Standard dev.)-0.000012864755 (±0.0001599504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 349.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Body 1 of 86-pRNP (HDAg 86-pRNA). Sharpened with...

Fileemd_71807_additional_1.map
AnnotationBody 1 of 86-pRNP (HDAg 86-pRNA). Sharpened with tightTarger DeepEMhancer protocol.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Body 1 of 86-pRNP (HDAg 86-pRNA). Half map - A.

Fileemd_71807_half_map_1.map
AnnotationBody 1 of 86-pRNP (HDAg 86-pRNA). Half map - A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Body 1 of 86-pRNP (HDAg 86-pRNA). Half map - B.

Fileemd_71807_half_map_2.map
AnnotationBody 1 of 86-pRNP (HDAg 86-pRNA). 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 : Complex of S-HDAg bound to 86-pRNA

EntireName: Complex of S-HDAg bound to 86-pRNA
Components
  • Complex: Complex of S-HDAg bound to 86-pRNA
    • Complex: S-HDAg
      • Protein or peptide: Small delta antigen
    • Complex: 86-pRNA
      • RNA: Palindromic RNA

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Supramolecule #1: Complex of S-HDAg bound to 86-pRNA

SupramoleculeName: Complex of S-HDAg bound to 86-pRNA / 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: 86-pRNA

SupramoleculeName: 86-pRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: Small delta antigen

MacromoleculeName: Small delta antigen / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis delta virus
Molecular weightTheoretical: 21.854631 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SRPEGRKNRG GREEVLEQWV SGRKKLEELE RDLRKVKKKI KKLEDEHPWL GNIKGILGKK DKDGEGAPPA KRARTDQMEV DSGPRKRPS RGGFTDKERQ DHRRRKALEN KRKQLSAGGK NLSKEEEEEL RRLTEEDERR ERRIAGPQVG GVNPLEGGTR G APGGGFVP ...String:
SRPEGRKNRG GREEVLEQWV SGRKKLEELE RDLRKVKKKI KKLEDEHPWL GNIKGILGKK DKDGEGAPPA KRARTDQMEV DSGPRKRPS RGGFTDKERQ DHRRRKALEN KRKQLSAGGK NLSKEEEEEL RRLTEEDERR ERRIAGPQVG GVNPLEGGTR G APGGGFVP SMQGVPESPF TRTGEGLDIR GSQGFP

UniProtKB: Small delta antigen

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Macromolecule #2: Palindromic RNA

MacromoleculeName: Palindromic RNA / type: rna / ID: 2
Details: 86-nucleotide palindromic RNA sequence. Residues from the T7 promoter (GGGAGA) and EcoRI restriction site (GAAUU) are added to start and end of sequence, respectively. The portions of RNA ...Details: 86-nucleotide palindromic RNA sequence. Residues from the T7 promoter (GGGAGA) and EcoRI restriction site (GAAUU) are added to start and end of sequence, respectively. The portions of RNA that could be traced in the map were modeled as poly(AU) due to uncertainty of residue identity.
Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.581357 KDa
SequenceString:
GGGAGAAUAU AUAUAUAUAU AUAUAUGUUU AUAUAUAUAU AUAUAUAUAU GAAUU

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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: FEI FALCON IV (4k 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: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1312415 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Details: Multibody refinement / Number images used: 298422
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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