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- EMDB-80928: Local refinement of the mpox virus A35R protein in complexed with... -

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Entry
Database: EMDB / ID: EMD-80928
TitleLocal refinement of the mpox virus A35R protein in complexed with 17H1 Fab
Map dataLocal refinement of the mpox virus A35R protein in complexed with 17H1 Fab
Sample
  • Complex: Local refinement of the mpox virus A35R protein in complexed with 17H1 Fab
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Variable domain of the 17H1 heavy chain
    • Protein or peptide: Variable domain of the 17H1 light chain
KeywordsImmune Complex / VIRAL PROTEIN
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / C-type lectin fold / host cell membrane / virion membrane / Protein OPG161
Function and homology information
Biological speciesMonkeypox virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsXiao YX / He MZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: MedComm (2020) / Year: 2026
Title: Discovery and Structural Characterization of a Highly Protective Neutralizing Antibody Targeting the Mpox Virus A35R Protein.
Authors: Shimeng Bai / Shuo Song / Xin Wang / Yuxin Xiao / Yun Long / Fenfang Wu / Fuxiang Wang / Zhongyi Fan / Jianqing Xu / Maozhou He / Hongzhou Lu /
Abstract: The recent resurgence of the mpox virus (MPXV) has raised global health concerns due to its potential to cause severe illness in vulnerable populations. Targeting the extracellular enveloped virus ...The recent resurgence of the mpox virus (MPXV) has raised global health concerns due to its potential to cause severe illness in vulnerable populations. Targeting the extracellular enveloped virus (EEV) protein A35R is a promising strategy to restrict viral dissemination within the host. In this study, we combined mRNA-LNP immunization with the Beacon Optofluidic system to rapidly screen and isolate high-affinity monoclonal antibodies. One of these antibodies, 17H1, exhibited exceptional neutralization against authentic MPXV. Cryo-electron microscopy (Cryo-EM) analysis revealed that 17H1 binds to a specific epitope at the distal ends of the A35R dimer. The interaction is stabilized by a unique network of hydrogen bonds and salt bridges, particularly involving residue E120, distinguishing its binding mode from previously reported A35R antibodies. Furthermore, 17H1 exhibited complete protective efficacy against MPXV infection in vivo and significantly reduced pulmonary viral load and lung pathogenesis. These findings highlight 17H1 as a promising therapeutic candidate for novel mpox interventions.
History
DepositionMay 18, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80928.png

Downloads & links

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Map

FileReleased
AnnotationLocal refinement of the mpox virus A35R protein in complexed with 17H1 Fab
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8
Minimum - Maximum-0.15904778 - 16.469100000000001
Average (Standard dev.)-0.002381172 (±0.23427682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_80928_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_80928_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of the mpox virus A35R protein in complexed with...

EntireName: Local refinement of the mpox virus A35R protein in complexed with 17H1 Fab
Components
  • Complex: Local refinement of the mpox virus A35R protein in complexed with 17H1 Fab
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Variable domain of the 17H1 heavy chain
    • Protein or peptide: Variable domain of the 17H1 light chain

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Supramolecule #1: Local refinement of the mpox virus A35R protein in complexed with...

SupramoleculeName: Local refinement of the mpox virus A35R protein in complexed with 17H1 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Monkeypox virus

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Macromolecule #1: Protein OPG161

MacromoleculeName: Protein OPG161 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 20.900422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MMTPENDEEQ TSVFSATVYG DKIQGKNKRK RVIGLCIRIS MVISLLSMIT MSAFLIVRLN QCMSANKAAI TDSAVAVAAA SSTHRKVVS STTQYDHKES CNGLYYQGSC YILHSDYKSF EDAKANCAAE SSTLPNKSDV LTTWLIDYVE DTWGSDGNPI T KTTSDYQD SDVSQEVRKY FCTHHHHHH

UniProtKB: Protein OPG161

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Macromolecule #2: Variable domain of the 17H1 heavy chain

MacromoleculeName: Variable domain of the 17H1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.816322 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLKQSGPE LVKPGASVKV SCKASGYAFT NYNMYWVKQS HGKSLEWIGY IDPYNGGTSY NQKFKGKVTL TVDKSSSTAY MHLNSLTSE DSAVYYCARR ASMDYWGQGT TLTVSSA

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Macromolecule #3: Variable domain of the 17H1 light chain

MacromoleculeName: Variable domain of the 17H1 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.934276 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS MYASLGESVT ITCKASQDIN SYLSWFQQKP GKSPKTLIYR ANRLVDGVPS RFSGSGSGQD YSLTISSLEY EDMGIYYCL QYDEFPYTFG GGTKLEIK

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 447301
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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