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- EMDB-38194: A35 of MPXV in complex with mAb981 -

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Basic information

Entry
Database: EMDB / ID: EMD-38194
TitleA35 of MPXV in complex with mAb981
Map data
Sample
  • Complex: A35 of MPXV in complex with mAb981
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Heavy chain of mAb981
    • Protein or peptide: Light chain of mAb981
KeywordsRECOMBINATION / REPLICATION / VIRAL PROTEIN
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / host cell membrane / C-type lectin fold / carbohydrate binding / virion membrane / membrane / Protein OPG161
Function and homology information
Biological speciesMonkeypox virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi YN / Shi TH / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: To Be Published
Title: Structure of MPXV A35 with a neutralizing and protective human monoclonal antibody
Authors: Li YN / Shi TH / Yan RH
History
DepositionDec 1, 2023-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38194.png

Downloads & links

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Map

FileDownload / File: emd_38194.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.904 Å		0.83 Å/pix.
x 288 pix.
= 239.904 Å		0.83 Å/pix.
x 288 pix.
= 239.904 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.78425854 - 1.6504273
Average (Standard dev.)0.0009943721 (±0.037325922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38194_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38194_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 : A35 of MPXV in complex with mAb981

EntireName: A35 of MPXV in complex with mAb981
Components
  • Complex: A35 of MPXV in complex with mAb981
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Heavy chain of mAb981
    • Protein or peptide: Light chain of mAb981

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Supramolecule #1: A35 of MPXV in complex with mAb981

SupramoleculeName: A35 of MPXV in complex with mAb981 / 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: 20.04342 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MMTPENDEEQ TSVFSATVYG DKIQGKNKRK RVIGLCIRIS MVISLLSMIT MSAFLIVRLN QCMSANEAAI TDSAVAVAAA SSTHRKVAS STTQYDHKES CNGLYYQGSC YILHSDYKSF EDAKANCAAE SSTLPNKSDV LTTWLIDYVE DTWGSDGNPI T KTTSDYQD SDVSQEVRKY FCT

UniProtKB: Protein OPG161

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Macromolecule #2: Heavy chain of mAb981

MacromoleculeName: Heavy chain of mAb981 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.548179 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLQLQESGPG LVKPSETLSL TCTVSGGSIS SNNDYWGWIR QPPGKGLEWI GSIYYSGRTN GNPSLKSRVN ISADTSKNQF SLKLNSVTA ADTAVYYCAR LRLGSLLHRY RAVDPWGQGI LVAVSS

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Macromolecule #3: Light chain of mAb981

MacromoleculeName: Light chain of mAb981 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.723094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERVT LSCRASQRVS STYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QHFDSSLLTF GGGTKVEIK

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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
VitrificationCryogen name: ETHANE

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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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 986061
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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