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- PDB-9lf8: Structure of MPXV M1R and mMM1-16 Fab complex -

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Basic information

Entry
Database: PDB / ID: 9lf8
TitleStructure of MPXV M1R and mMM1-16 Fab complex
Components
  • Entry-fusion complex associated protein OPG095
  • mMM1-16 Fab heavy chain
  • mMM1-16 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MPXV / neutralizing antibody / poxvirus / M1R / 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: 2.7 Å
AuthorsZhang, Y. / Zhao, R.C. / 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
DepositionJan 8, 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
E: mMM1-16 Fab light chain
R: Entry-fusion complex associated protein OPG095
F: mMM1-16 Fab heavy chain
C: mMM1-16 Fab light chain
D: mMM1-16 Fab heavy chain
S: Entry-fusion complex associated protein OPG095
L: mMM1-16 Fab light chain
H: mMM1-16 Fab heavy chain
Q: Entry-fusion complex associated protein OPG095
J: mMM1-16 Fab light chain
O: mMM1-16 Fab heavy chain
T: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)267,12212
Polymers267,12212
Non-polymers00
Water00
1
E: mMM1-16 Fab light chain
R: Entry-fusion complex associated protein OPG095
F: mMM1-16 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)66,7813
Polymers66,7813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: mMM1-16 Fab light chain
D: mMM1-16 Fab heavy chain
S: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)66,7813
Polymers66,7813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: mMM1-16 Fab light chain
H: mMM1-16 Fab heavy chain
Q: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)66,7813
Polymers66,7813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: mMM1-16 Fab light chain
O: mMM1-16 Fab heavy chain
T: Entry-fusion complex associated protein OPG095


Theoretical massNumber of molelcules
Total (without water)66,7813
Polymers66,7813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.378, 177.378, 90.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Antibody
mMM1-16 Fab light chain


Mass: 23551.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Protein
Entry-fusion complex associated protein OPG095 / EFC-associated protein OPG095 / Protein L1


Mass: 19306.670 Da / Num. of mol.: 4
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
#3: Antibody
mMM1-16 Fab heavy chain


Mass: 23922.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium fluoride, 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: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.7→49.2 Å / Num. obs: 150678 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 56.25 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.23
Reflection shellResolution: 2.7→2.7 Å / Num. unique obs: 24333 / CC1/2: 0.599

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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: 2.7→44.34 Å / SU ML: 0.3995 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2742 3850 5 %
Rwork0.2016 73163 -
obs0.2051 77013 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17006 0 0 0 17006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009417330
X-RAY DIFFRACTIONf_angle_d1.131223551
X-RAY DIFFRACTIONf_chiral_restr0.05892726
X-RAY DIFFRACTIONf_plane_restr0.00793011
X-RAY DIFFRACTIONf_dihedral_angle_d18.60846197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.37981360.31142604X-RAY DIFFRACTION99.38
2.73-2.770.3051360.2642586X-RAY DIFFRACTION100
2.77-2.80.36731380.2532612X-RAY DIFFRACTION100
2.8-2.840.34741360.25922592X-RAY DIFFRACTION100
2.84-2.880.34171370.24622604X-RAY DIFFRACTION100
2.88-2.930.33861370.2512602X-RAY DIFFRACTION100
2.93-2.970.30831360.25992584X-RAY DIFFRACTION100
2.97-3.020.3221380.25542617X-RAY DIFFRACTION100
3.02-3.070.31311350.25162559X-RAY DIFFRACTION100
3.07-3.130.29181370.23042614X-RAY DIFFRACTION100
3.13-3.190.31231360.21672586X-RAY DIFFRACTION100
3.19-3.250.27191380.21962611X-RAY DIFFRACTION100
3.25-3.320.30281380.21872631X-RAY DIFFRACTION100
3.32-3.40.28351370.2132593X-RAY DIFFRACTION100
3.4-3.490.25191370.20972614X-RAY DIFFRACTION100
3.49-3.580.29681370.21112592X-RAY DIFFRACTION99.96
3.58-3.690.2941370.21412615X-RAY DIFFRACTION100
3.69-3.810.26121370.20092605X-RAY DIFFRACTION100
3.81-3.940.29391370.20132597X-RAY DIFFRACTION100
3.94-4.10.24651390.18672638X-RAY DIFFRACTION100
4.1-4.290.26521380.17112618X-RAY DIFFRACTION100
4.29-4.510.20931370.1632613X-RAY DIFFRACTION100
4.51-4.790.21171380.15812618X-RAY DIFFRACTION100
4.79-5.160.25991380.15682620X-RAY DIFFRACTION100
5.16-5.680.26451390.17892642X-RAY DIFFRACTION100
5.68-6.50.27411390.19752639X-RAY DIFFRACTION100
6.5-8.180.26481400.2092666X-RAY DIFFRACTION100
8.19-44.340.27161420.19722691X-RAY DIFFRACTION98.71

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