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- PDB-9xjk: Structure of neutralizing antibody B9 with MPXV M1R -

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Basic information

Entry
Database: PDB / ID: 9xjk
TitleStructure of neutralizing antibody B9 with MPXV M1R
Components
  • B9 heavy chain
  • B9 light chain
  • Entry-fusion complex associated protein OPG095
KeywordsANTIVIRAL PROTEIN / Cryo-EM / Complex
Function / homologyVirion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / Entry-fusion complex associated protein OPG095
Function and homology information
Biological speciesMonkeypox virus
Macaca fascicularis (crab-eating macaque)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZai, X.D. / Chen, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other private2023QNRC001 China
CitationJournal: To Be Published
Title: Structure of neutralizing antibody B9 with MPXV M1R
Authors: Zai, X.D. / Chen, L.
History
DepositionNov 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Entry-fusion complex associated protein OPG095
B: B9 heavy chain
C: B9 light chain


Theoretical massNumber of molelcules
Total (without water)66,7453
Polymers66,7453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Entry-fusion complex associated protein OPG095 / IMV membrane protein M1R / EFC-associated protein OPG095 / Protein L1


Mass: 20162.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG099, MPXVgp080 / Production host: Escherichia coli (E. coli) / References: UniProt: M1LBP0
#2: Antibody B9 heavy chain


Mass: 23528.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Homo sapiens (human)
#3: Antibody B9 light chain


Mass: 23054.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: B9 FAB_M1R COMPLEX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Monkeypox virus10244
31Macaca fascicularis (crab-eating macaque)9541
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 430638 / Symmetry type: POINT
RefinementHighest resolution: 3.46 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034656
ELECTRON MICROSCOPYf_angle_d0.6276344
ELECTRON MICROSCOPYf_dihedral_angle_d4.495655
ELECTRON MICROSCOPYf_chiral_restr0.044741
ELECTRON MICROSCOPYf_plane_restr0.006820

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