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- PDB-4lu5: Structure of murine IgG2a A20G2-Fab in complex with vaccinia anti... -

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Basic information

Entry
Database: PDB / ID: 4lu5
TitleStructure of murine IgG2a A20G2-Fab in complex with vaccinia antigen A33R at the resolution of 2.9 Angstroms
Components
  • A33R
  • Murine IgG2a A20G2 Heavy chain Fab domain
  • Murine IgG2a A20G2 Light chain Fab domain
KeywordsIMMUNE SYSTEM / IgG domain / antibody-antigen complex / Fv / CH1 / IgG2a / antigen-binding fragment (Fab) / A33R antigen / Papain digest of the mAb / EEV membrane (outer membrane of vaccinia EV form)
Function / homology
Function and homology information


host cell membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Chordopoxvirus A33R / Chordopoxvirus A33R protein / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesVaccinia virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMatho, M.H. / Schlossman, A.M. / Zajonc, D.M.
CitationJournal: Plos Pathog. / Year: 2015
Title: Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer.
Authors: Matho, M.H. / Schlossman, A. / Meng, X. / Benhnia, M.R. / Kaever, T. / Buller, M. / Doronin, K. / Parker, S. / Peters, B. / Crotty, S. / Xiang, Y. / Zajonc, D.M.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A33R
B: A33R
H: Murine IgG2a A20G2 Heavy chain Fab domain
I: Murine IgG2a A20G2 Heavy chain Fab domain
L: Murine IgG2a A20G2 Light chain Fab domain
M: Murine IgG2a A20G2 Light chain Fab domain


Theoretical massNumber of molelcules
Total (without water)116,7026
Polymers116,7026
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.900, 157.261, 175.890
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: Protein A33R / EEV glycoprotein / EEV membrane glycoprotein / EEV membrane phosphoglycoprotein / VACV-DUKE-164 / VACV152


Mass: 11049.040 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 89-185) / Mutation: S89M, L118M, K123A, L140M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Plasmid: pNAN::A33 (90-185) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71TT1
#2: Antibody Murine IgG2a A20G2 Heavy chain Fab domain


Mass: 23134.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C
Description: musculus B-cell Fusion of SP2/0 myeloma cell line with splenocytes
Cell: Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Murine IgG2a A20G2 Light chain Fab domain


Mass: 24166.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C
Description: musculus B-cell Fusion of SP2/0 myeloma cell line with splenocytes
Cell: Hybridoma / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS PROVIDED SEQUENCE DATABASE REFERENCES: A20G2 ANTIBODY HEAVY CHAIN GI 563323196, ACCESSION ...AUTHORS PROVIDED SEQUENCE DATABASE REFERENCES: A20G2 ANTIBODY HEAVY CHAIN GI 563323196, ACCESSION KF648646, A20G2 ANTIBODY LIGHT CHAIN GI 563323198, ACCESSION KF648647.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350 (w/v), 8% tacsimate (v/v), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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
Details: Monochromator Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs, Crystal Type Si(111), Mirrors Rh coated flat mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→54.94 Å / Num. all: 31632 / Num. obs: 30937 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.228 / Rsym value: 0.228 / Net I/σ(I): 5.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2 / Rsym value: 0.751 / % possible all: 93.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→54.94 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.849 / SU B: 18.615 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28157 1556 5.1 %RANDOM
Rwork0.23435 ---
obs0.23678 29233 97.23 %-
all-30131 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7949 0 0 59 8008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.028144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.95511086
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2951020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9324.277325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.763151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8881532
X-RAY DIFFRACTIONr_chiral_restr0.0650.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216102
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 93 -
Rwork0.302 2027 -
obs--92.41 %

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