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- EMDB-62650: A35 of MPXV in complex with mAb975 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62650
TitleA35 of MPXV in complex with mAb975
Map data
Sample
  • Complex: A35 of MPXV in complex with mAb975
    • Protein or peptide: mab975HC
    • Protein or peptide: mab975KC
  • Protein or peptide: Protein OPG161
Keywordsenvelope glycoprotein / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / host cell membrane / C-type lectin fold / virion membrane / membrane / Protein OPG161
Function and homology information
Biological speciesHomo sapiens (human) / Monkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYan RH / Yang HN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A35 of MPXV in complex with mAb975
Authors: Yan RH / Yang HN
History
DepositionDec 9, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62650.png

Downloads & links

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Map

FileDownload / File: emd_62650.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å		0.83 Å/pix.
x 320 pix.
= 264.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.22021505 - 0.8347716
Average (Standard dev.)0.0016647483 (±0.024092654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62650_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_62650_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 mAb975

EntireName: A35 of MPXV in complex with mAb975
Components
  • Complex: A35 of MPXV in complex with mAb975
    • Protein or peptide: mab975HC
    • Protein or peptide: mab975KC
  • Protein or peptide: Protein OPG161

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Supramolecule #1: A35 of MPXV in complex with mAb975

SupramoleculeName: A35 of MPXV in complex with mAb975 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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: 9.261993 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CNGLYYQGSC YILHSDYKSF EDAKANCAAE SSTLPNKSDV LTTWLIDYVE DTWGSDGNPI TKTTSDYQDS DVSQEVRKYF CT

UniProtKB: Protein OPG161

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Macromolecule #2: mab975HC

MacromoleculeName: mab975HC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.109636 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLQESGPGL VKPSGTLSLT CAVSRASISS SNWWSWLRQP PGKGLEWIGE IFHSGSTNYN PSLRSRVTIS VDKSKNQFSL NVSSVTAAD TAVYYCARSQ GGSGLFRAKW FDPWGQGTLV TV

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Macromolecule #3: mab975KC

MacromoleculeName: mab975KC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.298476 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQHK PGQAPRLLMY GASSRAPGTP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPRTF GQGTKV

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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: 7.5
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: 1.5 µm / Nominal defocus min: 0.8 µm
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: PDB ENTRY
PDB model - PDB ID:

8xa4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180429
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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