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- PDB-8xa4: A35 of MPXV in complex with mAb981 -

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Basic information

Entry
Database: PDB / ID: 8xa4
TitleA35 of MPXV in complex with mAb981
Components
  • Heavy chain of mAb981
  • Light chain of mAb981
  • Protein OPG161
KeywordsVIRAL PROTEIN / RECOMBINATION / REPLICATION
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi, Y.N. / Shi, T.H. / Yan, R.H.
Funding support China, 1items
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, Y.N. / Shi, T.H. / Yan, R.H.
History
DepositionDec 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein OPG161
B: Protein OPG161
C: Heavy chain of mAb981
D: Light chain of mAb981


Theoretical massNumber of molelcules
Total (without water)65,3584
Polymers65,3584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-18 kcal/mol
Surface area17280 Å2

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Components

#1: Protein Protein OPG161


Mass: 20043.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: A35R / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q80KX2
#2: Protein Heavy chain of mAb981


Mass: 13548.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain of mAb981


Mass: 11723.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / 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: A35 of MPXV in complex with mAb981 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 986061 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033111
ELECTRON MICROSCOPYf_angle_d0.5014230
ELECTRON MICROSCOPYf_dihedral_angle_d4.091431
ELECTRON MICROSCOPYf_chiral_restr0.039467
ELECTRON MICROSCOPYf_plane_restr0.004542

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