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- PDB-8zu9: The complex structure of MPXV M1R and neutralizing antibody A129 -

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Basic information

Entry
Database: PDB / ID: 8zu9
TitleThe complex structure of MPXV M1R and neutralizing antibody A129
Components
  • A129 heavy chain
  • A129 light chain
  • Entry-fusion complex associated protein OPG095
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / complex / antigen / antibody / ANTIVIRAL PROTEIN-IMMUNE SYSTEM 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 / membrane / Entry-fusion complex associated protein OPG095
Function and homology information
Biological speciesHomo sapiens (human)
Monkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsGe, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The complex structure of MPXV M1R and neutralizing antibody A129
Authors: Ge, J.W.
History
DepositionJun 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: A129 heavy chain
A: A129 light chain
E: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)67,1193
Polymers67,1193
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.730, 89.300, 100.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody A129 heavy chain


Mass: 23777.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody A129 light chain


Mass: 23187.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Entry-fusion complex associated protein OPG095 / MPXV M1R / EFC-associated protein OPG095 / Protein L1


Mass: 20153.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG099, MPXVgp080 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: M1LBP0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium citrate tribasic tetrahydrate, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.17→50.37 Å / Num. obs: 36315 / % possible obs: 99.91 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.9
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 1.267 / Num. unique obs: 3566

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata processing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I9L

2i9l


Resolution: 2.17→38.33 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 2000 5.51 %
Rwork0.2113 --
obs0.2141 36315 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 0 111 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124646
X-RAY DIFFRACTIONf_angle_d1.4116319
X-RAY DIFFRACTIONf_dihedral_angle_d12.518638
X-RAY DIFFRACTIONf_chiral_restr0.065729
X-RAY DIFFRACTIONf_plane_restr0.008817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.220.3221390.2722388X-RAY DIFFRACTION100
2.22-2.280.31891420.26252447X-RAY DIFFRACTION100
2.28-2.350.32011410.25442407X-RAY DIFFRACTION100
2.35-2.430.30891410.24962414X-RAY DIFFRACTION100
2.43-2.510.32951410.23512427X-RAY DIFFRACTION100
2.51-2.610.32711430.24812438X-RAY DIFFRACTION100
2.61-2.730.28941400.23022409X-RAY DIFFRACTION100
2.73-2.880.29951420.23542449X-RAY DIFFRACTION100
2.88-3.060.28941430.22762451X-RAY DIFFRACTION100
3.06-3.290.28111420.22052429X-RAY DIFFRACTION100
3.29-3.630.24291430.19742465X-RAY DIFFRACTION100
3.63-4.150.2521450.18632478X-RAY DIFFRACTION100
4.15-5.230.21761450.17642501X-RAY DIFFRACTION100
5.23-38.330.23471530.21272612X-RAY DIFFRACTION100

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