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- EMDB-66938: Structure of neutralizing antibody B9 with MPXV M1R -

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Basic information

Entry
Database: EMDB / ID: EMD-66938
TitleStructure of neutralizing antibody B9 with MPXV M1R
Map data
Sample
  • Complex: B9 FAB_M1R COMPLEX
    • Protein or peptide: Entry-fusion complex associated protein OPG095
    • Protein or peptide: B9 heavy chain
    • Protein or peptide: B9 light chain
KeywordsCryo-EM / Complex / ANTIVIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZai XD / Chen L
Funding support China, 1 items
OrganizationGrant numberCountry
Other private2023QNRC001 China
CitationJournal: To Be Published
Title: Structure of neutralizing antibody B9 with MPXV M1R
Authors: Zai XD / Chen L
History
DepositionNov 4, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66938.png

Downloads & links

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Map

FileDownload / File: emd_66938.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.0016902902 - 1.8378226
Average (Standard dev.)0.0011246982 (±0.02470705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66938_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66938_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : B9 FAB_M1R COMPLEX

EntireName: B9 FAB_M1R COMPLEX
Components
  • Complex: B9 FAB_M1R COMPLEX
    • Protein or peptide: Entry-fusion complex associated protein OPG095
    • Protein or peptide: B9 heavy chain
    • Protein or peptide: B9 light chain

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Supramolecule #1: B9 FAB_M1R COMPLEX

SupramoleculeName: B9 FAB_M1R COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Monkeypox virus

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Macromolecule #1: Entry-fusion complex associated protein OPG095

MacromoleculeName: Entry-fusion complex associated protein OPG095 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 20.16251 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHGAAA SIQTTVNTLS ERISSKLEQE ANASAQTKCD IEIGNFYIRQ NHGCNITVKN MCSADADAQL DAVLSAATET YSGLTPEQK AYVPAMFTAA LNIQTSVNTV VRDFENYVKQ TCNSSAVVDN KLKIQNVIID ECYGAPGSPT NLEFINTGSS K GNCAIKAL MQLTTKATTQ IAPRQVAGTG

UniProtKB: Entry-fusion complex associated protein OPG095

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Macromolecule #2: B9 heavy chain

MacromoleculeName: B9 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.528379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LAKPGGSLRL SCAASGFTLG GYAMHWVRQA PGKGLEWVSV IISGGTTYYA DSVQGRFTIS RDNSKNTLSL QMNSLRPED TAVYYCTLRV AATESYYSGL DSWGQGVVVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EVQLVESGGG LAKPGGSLRL SCAASGFTLG GYAMHWVRQA PGKGLEWVSV IISGGTTYYA DSVQGRFTIS RDNSKNTLSL QMNSLRPED TAVYYCTLRV AATESYYSGL DSWGQGVVVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Macromolecule #3: B9 light chain

MacromoleculeName: B9 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.054432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QPVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYGVQWYQQ LPGTAPKLLI YENNKRPSGV SDRFSGSQSG TSASLTITGL QSEDEADYY CQSYDSSLSA HVLFGGGTRL TVLGQPKANP TVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADGS P VKAGVETT ...String:
QPVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYGVQWYQQ LPGTAPKLLI YENNKRPSGV SDRFSGSQSG TSASLTITGL QSEDEADYY CQSYDSSLSA HVLFGGGTRL TVLGQPKANP TVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADGS P VKAGVETT KPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TITAN THEMIS
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: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 430638
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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