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- PDB-9vhz: Structure of MPXV M1R and hmMM1-40 Fab complex -

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Basic information

Entry
Database: PDB / ID: 9vhz
TitleStructure of MPXV M1R and hmMM1-40 Fab complex
Components
  • Entry-fusion complex associated protein OPG095
  • hmMM1-40 Fab heavy chain
  • hmMM1-40 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MPXV / neutralizing antibody / poxvirus / M1R / VIRAL PROTEIN / VIRAL 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 speciesMus musculus (house mouse)
Monkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhao, R.C. / Zhang, Y. / Wu, L.L. / Wang, Q.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Embo Mol Med / Year: 2025
Title: Anti-M1R/B6R antibody characterization and bispecific design for enhanced orthopoxvirus protection.
Authors: Zhao, R. / Wu, L. / Zhang, Y. / Ma, J. / Liu, D. / Zheng, Y. / Kong, T. / Ma, R. / Gao, Z. / Chai, Y. / Liu, Y. / Tian, Y. / Xia, Y. / Hou, Y. / Lu, J. / Cong, Z. / Huang, B. / Tan, W. / ...Authors: Zhao, R. / Wu, L. / Zhang, Y. / Ma, J. / Liu, D. / Zheng, Y. / Kong, T. / Ma, R. / Gao, Z. / Chai, Y. / Liu, Y. / Tian, Y. / Xia, Y. / Hou, Y. / Lu, J. / Cong, Z. / Huang, B. / Tan, W. / Xue, J. / Gao, G.F. / Wang, Q.
History
DepositionJun 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hmMM1-40 Fab heavy chain
B: hmMM1-40 Fab light chain
Q: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)69,3413
Polymers69,3413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.361, 72.353, 170.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody hmMM1-40 Fab heavy chain


Mass: 25901.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody hmMM1-40 Fab light chain


Mass: 24132.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Entry-fusion complex associated protein OPG095 / EFC-associated protein OPG095 / Protein L1


Mass: 19306.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG099, MPXVgp080 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1LBP0
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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.05 M HEPES sodium pH 7.0, 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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→85.29 Å / Num. obs: 18631 / % possible obs: 96 % / Redundancy: 7.3 % / CC1/2: 0.986 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 949 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→55.18 Å / SU ML: 0.4532 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2957 893 4.82 %
Rwork0.2075 17647 -
obs0.2118 18540 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→55.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 0 0 4629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034723
X-RAY DIFFRACTIONf_angle_d1.15526419
X-RAY DIFFRACTIONf_chiral_restr0.0576736
X-RAY DIFFRACTIONf_plane_restr0.0094824
X-RAY DIFFRACTIONf_dihedral_angle_d6.4282650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.34191460.282971X-RAY DIFFRACTION99.49
2.98-3.210.38111610.29033011X-RAY DIFFRACTION100
3.21-3.530.341390.24252755X-RAY DIFFRACTION90.89
3.53-4.040.35751250.22612599X-RAY DIFFRACTION84.47
4.04-5.090.23581620.16913074X-RAY DIFFRACTION100
5.09-55.180.26521600.17983237X-RAY DIFFRACTION99.82

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