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- EMDB-71806: Twisted arrangement of the HDV 311-RNP, Multibody refinement, Body 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-71806
TitleTwisted arrangement of the HDV 311-RNP, Multibody refinement, Body 1
Map dataTwisted arrangement of 311-RNP, Multibody refined Body 1. Unsharpened.
Sample
  • Complex: Twisted 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 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-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71806.png

Downloads & links

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Map

FileDownload / File: emd_71806.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTwisted arrangement of 311-RNP, Multibody refined Body 1. 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: 0.0054
Minimum - Maximum-0.014231884 - 0.022554759
Average (Standard dev.)-0.0000045227684 (±0.00051741826)
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: Twisted arrangement of 311-RNP, Multibody refined Body 1....

Fileemd_71806_half_map_1.map
AnnotationTwisted arrangement of 311-RNP, Multibody refined Body 1. Half map - B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Twisted arrangement of 311-RNP, Multibody refined Body 1....

Fileemd_71806_half_map_2.map
AnnotationTwisted arrangement of 311-RNP, Multibody refined Body 1. Half map - A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Twisted arrangement map of S-HDAg bound to 311-agRNA
Components
  • Complex: Twisted 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: Twisted arrangement map of S-HDAg bound to 311-agRNA

SupramoleculeName: Twisted 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 HindIII 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: RELION (ver. 5.0) / Details: Multibody refinement from RELION / Number images used: 43959
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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