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- PDB-4etq: Vaccinia virus D8L IMV envelope protein in complex with Fab of mu... -

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Basic information

Entry
Database: PDB / ID: 4etq
TitleVaccinia virus D8L IMV envelope protein in complex with Fab of murine IgG2a LA5
Components
  • (anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, ...) x 2
  • IMV membrane protein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / variable domain / constant domain / IgG2a / IgG domain / CDR / hypervariable region / neutralizing antibody / beta sheet / carbonic anhydrase fold / loose knot / chondroitin-sulfate binding site / delta 262 / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


carbonate dehydratase activity / virion membrane / zinc ion binding / membrane
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Roll ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Cell surface-binding protein OPG105
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMatho, M.H. / Zajonc, D.M.
CitationJournal: J.Virol. / Year: 2012
Title: Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5.
Authors: Matho, M.H. / Maybeno, M. / Benhnia, M.R. / Becker, D. / Meng, X. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain
L: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain
A: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain
B: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain
X: IMV membrane protein
C: IMV membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,82717
Polymers157,1056
Non-polymers72211
Water8,863492
1
H: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain
L: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain
C: IMV membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8588
Polymers78,5533
Non-polymers3065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain
B: anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain
X: IMV membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9699
Polymers78,5533
Non-polymers4176
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.021, 91.156, 103.774
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules XC

#3: Protein IMV membrane protein / D8L IMV envelope protein


Mass: 31321.184 Da / Num. of mol.: 2 / Fragment: UNP residues 1-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Acam2000 / Gene: D8L, VACAC2_124, VACCL3_124, VAC_DPP17_124 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1M1K6

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Antibody , 2 types, 4 molecules HALB

#1: Antibody anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain


Mass: 23926.680 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c
Description: BALB/c splenocytes fused with mouse myeloma SP2/0 cells
Cell: hybridoma / Gene: IgG2a, IGHV1S127*01
#2: Antibody anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain


Mass: 23304.697 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c
Description: BALB/c splenocytes fused with mouse myeloma SP2/0 cells
Cell: hybridoma / Gene: IgG2a, IGKV4-55*01 germ line

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Non-polymers , 5 types, 503 molecules

#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2010
Details: Sample to detector distance: 185-650 mm, maximum vertical offset: 208 mm
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 77173 / % possible obs: 97.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.086 / Χ2: 2.235 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1830.45973231.393193.2
2.18-2.263.10.39676681.43197.7
2.26-2.373.10.33878121.521199.3
2.37-2.493.10.28478071.605199.7
2.49-2.653.10.21678211.852199.4
2.65-2.853.10.15977892.204199.1
2.85-3.143.10.11478112.705198.6
3.14-3.593.10.08177383.184198.2
3.59-4.523.20.06277343.535197.4
4.52-403.20.04776702.736195.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å36.2 Å
Translation4 Å36.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1NSN AND 3JXF

1nsn

3jxf


Resolution: 2.1→36.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.2046 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.808 / SU B: 13.442 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2573 / SU Rfree: 0.2087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1533 2 %RANDOM
Rwork0.2016 ---
obs0.2026 77145 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.02 Å2 / Biso mean: 42.432 Å2 / Biso min: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10196 0 39 492 10727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210583
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.94714432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97351327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08424.414444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.923151674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4851535
X-RAY DIFFRACTIONr_chiral_restr0.0730.21605
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218024
X-RAY DIFFRACTIONr_mcbond_it0.3761.56597
X-RAY DIFFRACTIONr_mcangle_it0.693210709
X-RAY DIFFRACTIONr_scbond_it1.06133986
X-RAY DIFFRACTIONr_scangle_it1.6124.53715
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 90 -
Rwork0.268 5221 -
all-5311 -
obs--91.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9070.3672-0.30352.3955-1.14744.9262-0.1401-0.0670.11150.1050.08650.1659-0.4197-0.25230.05360.16120.1133-0.08830.1339-0.03740.1742-6.74219.458122.3345
22.21780.09490.01386.5081.9122.9263-0.00140.1166-0.2062-0.1652-0.0773-0.01140.17660.0420.07870.063-0.0259-0.03410.04020.02980.0691-4.42824.8885-11.0162
30.5623-0.6921-0.17472.9162.58413.283-0.0923-0.1262-0.04680.04860.04360.13990.1514-0.02320.04870.09450.0445-0.03520.07540.00730.10861.8329-11.056921.0054
40.8180.3047-0.49136.9825-3.80035.15840.06230.08850.0668-0.3707-0.3066-0.84660.01680.6620.24430.1190.0190.05670.18510.04090.226510.1415-1.8113-13.6779
52.99970.143-0.69893.3961-0.31253.52220.1048-0.29490.17290.1255-0.17310.1083-0.2395-0.10310.06830.0704-0.00540.03050.2125-0.040.09743.972127.781898.6338
60.86451.1325-0.9162.5229-2.1993.89470.04630.03180.1210.3520.07730.17-0.3892-0.2248-0.12350.16470.06540.01410.0531-0.0140.069913.674432.519771.1828
71.47530.1506-0.54817.57522.01691.9706-0.05190.2465-0.1635-0.33340.00680.28920.0841-0.13070.0450.0445-0.0312-0.03830.0850.01510.076818.744628.4538.3794
80.7692-0.3681-0.72733.04691.70183.59120.0295-0.0227-0.10360.06340.0034-0.0735-00.0189-0.03290.0189-0.0027-0.02860.02190.00820.051422.524412.275370.5238
90.79920.733-1.08735.1746-3.53244.28970.07180.0360.0004-0.2686-0.2463-0.4195-0.02490.42630.17450.0553-0.0020.02140.1197-0.01380.080133.222721.851436.4134
102.9688-1.12910.30335.0949-0.68865.23420.0587-0.2027-0.06220.10290.02250.598-0.2398-0.5718-0.08110.05790.05890.00710.34470.01590.1926-11.90175.696151.0756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 119
2X-RAY DIFFRACTION2H120 - 219
3X-RAY DIFFRACTION3L2 - 107
4X-RAY DIFFRACTION4L108 - 212
5X-RAY DIFFRACTION5X2 - 236
6X-RAY DIFFRACTION6A2 - 119
7X-RAY DIFFRACTION7A120 - 219
8X-RAY DIFFRACTION8B2 - 107
9X-RAY DIFFRACTION9B108 - 212
10X-RAY DIFFRACTION10C3 - 235

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