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- PDB-8zua: The complex structure of MPXV M1R and neutralizing antibody A138 -

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Basic information

Entry
Database: PDB / ID: 8zua
TitleThe complex structure of MPXV M1R and neutralizing antibody A138
Components
  • A138 heavy chain
  • A138 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 / symbiont entry into host cell / viral envelope / 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: 3.49 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
A: A138 heavy chain
F: Entry-fusion complex associated protein OPG095
G: A138 light chain
B: A138 heavy chain
C: Entry-fusion complex associated protein OPG095
D: A138 light chain
E: A138 heavy chain
H: Entry-fusion complex associated protein OPG095
I: A138 light chain
J: A138 heavy chain
K: Entry-fusion complex associated protein OPG095
L: A138 light chain


Theoretical massNumber of molelcules
Total (without water)265,74912
Polymers265,74912
Non-polymers00
Water00
1
A: A138 heavy chain
F: Entry-fusion complex associated protein OPG095
G: A138 light chain


Theoretical massNumber of molelcules
Total (without water)66,4373
Polymers66,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A138 heavy chain
C: Entry-fusion complex associated protein OPG095
D: A138 light chain


Theoretical massNumber of molelcules
Total (without water)66,4373
Polymers66,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: A138 heavy chain
H: Entry-fusion complex associated protein OPG095
I: A138 light chain


Theoretical massNumber of molelcules
Total (without water)66,4373
Polymers66,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: A138 heavy chain
K: Entry-fusion complex associated protein OPG095
L: A138 light chain


Theoretical massNumber of molelcules
Total (without water)66,4373
Polymers66,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.390, 136.678, 123.769
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
A138 heavy chain


Mass: 23227.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein
Entry-fusion complex associated protein OPG095 / MPXV M1R / EFC-associated protein OPG095 / Protein L1


Mass: 20153.590 Da / Num. of mol.: 4
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
#3: Antibody
A138 light chain


Mass: 23055.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium formate dihydrate, 15% 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: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 33850 / % possible obs: 97.31 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.253 / Net I/σ(I): 5.4
Reflection shellResolution: 3.49→3.62 Å / Rmerge(I) obs: 0.779 / Num. unique obs: 3041

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I9L

2i9l


Resolution: 3.49→46.67 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 1563 4.62 %
Rwork0.2371 --
obs0.2394 33850 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17537 0 0 0 17537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817946
X-RAY DIFFRACTIONf_angle_d1.39824397
X-RAY DIFFRACTIONf_dihedral_angle_d15.7462478
X-RAY DIFFRACTIONf_chiral_restr0.0612837
X-RAY DIFFRACTIONf_plane_restr0.0083134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.60.36871190.29142551X-RAY DIFFRACTION84
3.6-3.730.31661190.27312847X-RAY DIFFRACTION94
3.73-3.880.321420.27542911X-RAY DIFFRACTION97
3.88-4.050.27641450.25212930X-RAY DIFFRACTION98
4.05-4.270.31611430.24123013X-RAY DIFFRACTION99
4.27-4.530.25731520.21192977X-RAY DIFFRACTION100
4.53-4.880.25741530.20863003X-RAY DIFFRACTION100
4.88-5.380.2351530.21132988X-RAY DIFFRACTION100
5.38-6.150.31971320.24733062X-RAY DIFFRACTION100
6.15-7.740.31171520.24983022X-RAY DIFFRACTION100
7.74-46.670.26551530.21552983X-RAY DIFFRACTION97

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