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- PDB-4u6h: Vaccinia L1/M12B9-Fab complex -

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Basic information

Entry
Database: PDB / ID: 4u6h
TitleVaccinia L1/M12B9-Fab complex
Components
  • Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9
  • Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9
  • Protein L1
KeywordsIMMUNE SYSTEM / IgG2a / Fab / heavy chain light chain
Function / homology
Function and homology information


symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Entry-fusion complex associated protein OPG095
Similarity search - Component
Biological speciesVaccinia virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMatho, M.H. / Schlossman, A. / Zajonc, D.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200900048C United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41GM103393 United States
CitationJournal: J.Virol. / Year: 2014
Title: Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in l1 protein.
Authors: Kaever, T. / Meng, X. / Matho, M.H. / Schlossman, A. / Li, S. / Sela-Culang, I. / Ofran, Y. / Buller, M. / Crump, R.W. / Parker, S. / Frazier, A. / Crotty, S. / Zajonc, D.M. / Peters, B. / Xiang, Y.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / entity_src_nat ...entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9
B: Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9
C: Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9
D: Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9
E: Protein L1
J: Protein L1


Theoretical massNumber of molelcules
Total (without water)134,7986
Polymers134,7986
Non-polymers00
Water0
1
A: Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9
B: Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9
E: Protein L1


Theoretical massNumber of molelcules
Total (without water)67,3993
Polymers67,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9
D: Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9
J: Protein L1


Theoretical massNumber of molelcules
Total (without water)67,3993
Polymers67,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.829, 102.829, 238.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9


Mass: 23757.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: splenocyte / Organ: spleen / Plasmid details: fusion with mouse myeloma SP2/0 cells / Strain: Balb/c
#2: Antibody Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9


Mass: 24105.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Splenocyte / Organ: Spleen
Plasmid details: splenocytes fused with the mouse myeloma SP2/0 cells
Strain: Balb/c
#3: Protein Protein L1 / Virion membrane protein M25


Mass: 19535.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: VACWR088, L1R / Plasmid: pML1 / Details (production host): same as for entry 1YPY / Production host: Escherichia coli (E. coli) / References: UniProt: P07612

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Initial crystallization experiments were carried out by sitting-drop vapor diffusion in a 96-well format, using a Phoenix liquid-handling robot with a panel of commercial sparse-matrix ...Details: Initial crystallization experiments were carried out by sitting-drop vapor diffusion in a 96-well format, using a Phoenix liquid-handling robot with a panel of commercial sparse-matrix screens (PEG/Ion 1 and 2 from Hampton Research, Wizard 2 from Emerald Biosciences, JCSG Plus Suite from Qiagen, and JBScreen 6 from Jena BioScience). Quality diffracting crystals of L1/M12B9-Fab complex were obtained at RT by mixing 0.5ul of protein solution at 9.5 mg/ml with 0.5ul of precipitant [100 mM Tris, pH 7.0, 20% (w/v) polyethylene glycol (PEG) 3000, and 200 mM Ca(OAc)] and seeding with initial crystals obtained at 6.5 mg/ml. Crystal were flash-frozen at 100K in mother liquor containing 20 % glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.1→47.67 Å / Num. obs: 27308 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 9.2 % / Rmerge(I) obs: 0.2 / Rsym value: 0.077 / Net I/σ(I): 9.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPY,1SY6

1ypy

1sy6


Resolution: 3.1→47.21 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.871 / SU B: 23.379 / SU ML: 0.395 / Cross valid method: FREE R-VALUE / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26491 1367 5 %RANDOM
Rwork0.20938 ---
obs0.21221 25898 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 3.1→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 0 0 9188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.029392
X-RAY DIFFRACTIONr_bond_other_d0.0010.028659
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.94512790
X-RAY DIFFRACTIONr_angle_other_deg0.6443.00319984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96451195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01725.053380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.955151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5811532
X-RAY DIFFRACTIONr_chiral_restr0.0510.21475
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022095
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 100 -
Rwork0.313 1862 -
obs--99.9 %

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