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- PDB-4lqf: Structure of murine IgG2b A2C7-Fab in complex with vaccinia antig... -

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Basic information

Entry
Database: PDB / ID: 4lqf
TitleStructure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at the resolution of 2.3 Angstroms
Components
  • A33R
  • Murine IgG2b A2C7 Heavy chain Fab domain
  • Murine IgG2b A2C7 Light chain Fab domain
KeywordsIMMUNE SYSTEM / IgG domain / antibody-antigen complex / Fv / CH1 / IgG2b / 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: 2.3 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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Mar 18, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_prop ...pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
A: A33R
H: Murine IgG2b A2C7 Heavy chain Fab domain
L: Murine IgG2b A2C7 Light chain Fab domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6837
Polymers58,4223
Non-polymers2624
Water1,45981
1
A: A33R
H: Murine IgG2b A2C7 Heavy chain Fab domain
L: Murine IgG2b A2C7 Light chain Fab domain
hetero molecules

A: A33R
H: Murine IgG2b A2C7 Heavy chain Fab domain
L: Murine IgG2b A2C7 Light chain Fab domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,36714
Polymers116,8436
Non-polymers5238
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)71.280, 73.180, 221.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 1 / 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 IgG2b A2C7 Heavy chain Fab domain


Mass: 23137.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: B-cellB cell
Description: Fusion of SP2/0 myeloma cell line with splenocytes
Cell: Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Murine IgG2b A2C7 Light chain Fab domain


Mass: 24234.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: B-cellB cell
Description: Fusion of SP2/0 myeloma cell line with splenocytes
Cell: Hybridoma / Production host: Mus musculus (house mouse)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS PROVIDED SEQUENCE DATABASE REFERENCES: ANTI A33 VACCINIA ANTIBODY IGG2B A2C7 HEAVY CHAIN GI ...AUTHORS PROVIDED SEQUENCE DATABASE REFERENCES: ANTI A33 VACCINIA ANTIBODY IGG2B A2C7 HEAVY CHAIN GI 563323188, ACCESSION KF648642. ANTI A33 VACCINIA ANTIBODY IGG2B A2C7 LIGHT CHAIN GI 563323190, ACCESSION KF648643.

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG3000, 0.1M imidazole, 0.2M zinc acetate, pH 8.0, 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: 2.3→49.76 Å / Num. all: 26224 / Num. obs: 25343 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2 / Rsym value: 0.644 / % possible all: 90.9

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHASERphasing
REFMAC5.7.0029refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A20G2-Fv domain (reported in same publication), conserved domain of 3E5 IgG3 Fab (extracted from pdb entry 4HDI), one monomer of A33 (extracted from pdb entry 3K7B)

4hdi

3k7b


Resolution: 2.3→49.76 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.606 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23046 1283 5.1 %RANDOM
Rwork0.1973 ---
obs0.19897 23980 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.391 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---1.75 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 4 81 3990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024006
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9425460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07524.188160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39315627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1841515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213014
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 89 -
Rwork0.127 1606 -
obs--89.3 %
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)
18.9752-2.24714.76030.8772-0.12798.3584-0.1285-0.2262-0.04510.10130.2389-0.17420.04970.9489-0.11030.05810.0162-0.05620.21440.00030.24477.017632.8127-4.2985
24.66721.7304-1.31862.61480.62524.265-0.05590.1645-0.0503-0.2382-0.04150.04750.0315-0.03080.09740.085-0.0189-0.01780.0582-0.00210.0076-3.947530.8686-14.4385
31.42032.5719-2.25814.64783.48749.4558-0.1922-0.0063-0.09310.8741-0.01930.16461.2938-0.04450.21150.3380.0724-0.09740.21620.07980.27740.08621.3195-0.0116
42.7633.41723.15654.25593.91173.60930.3444-0.2379-0.14990.3844-0.2073-0.15820.3579-0.2611-0.13710.0666-0.0275-0.04460.18570.05360.0435-8.476926.5106-5.0601
50.56181.42860.98156.53050.58092.98030.00710.1256-0.0734-0.0066-0.1041-0.52220.02060.49820.0970.0696-0.0139-0.01240.16520.00840.06250.038231.6147-9.3958
61.8266-0.6720.08493.1348-4.343711.3885-0.0508-0.12440.14210.25830.26290.3501-0.2515-0.5605-0.21220.0410.01770.01430.1167-0.04850.1589-36.35437.6342-20.6818
73.47360.06031.79851.1206-0.70513.4721-0.070.11220.17370.07310.01460.07290.0498-0.05760.05550.0168-0.0170.00950.0546-0.03470.0495-25.587432.093-21.5634
81.7097-0.49691.54141.9107-1.08792.3295-0.039-0.09220.23610.0683-0.08230.1193-0.20470.01590.12120.0343-0.01830.00610.0878-0.05740.0916-30.72135.6437-22.9189
92.15660.41240.21265.75660.04212.61940.0197-0.06620.0040.17030.0035-0.05880.0187-0.0733-0.02320.04710.0342-0.01910.1218-0.01790.0701-54.280127.2673-45.8269
102.05050.56130.89734.0130.22621.0793-0.0721-0.18240.1692-0.10660.03330.6095-0.2047-0.41850.03870.09330.0526-0.00210.21620.00420.1135-62.167926.5342-46.2562
112.61010.65330.54411.83920.18131.66960.06010.0457-0.1124-0.00180.00750.05520.2131-0.0812-0.06750.0512-0.0216-0.00940.0568-0.00640.0272-27.08112.8778-23.974
1213.33719.27397.80846.81926.08426.0551-0.33070.07240.3171-0.15980.08520.35690.0514-0.02650.24540.0773-0.023-0.04680.0910.09040.1595-33.145214.3855-31.5906
130.4080.35020.18672.801-1.92041.99590.03070.0833-0.0411-0.0747-0.0826-0.14480.07330.08890.05180.06240.0162-0.0550.08290.00010.0881-48.862418.5254-54.6957
140.6623-0.61511.79884.7284-2.76175.1911-0.0140.14820.00690.016-0.020.0352-0.13670.39710.0340.17020.0003-0.0630.149-0.01250.1356-43.44518.4871-48.0811
150.79850.28880.01741.3244-0.80082.62710.03470.11080.0112-0.3453-0.0241-0.09750.086-0.0752-0.01060.14140.0186-0.00790.1408-0.00570.1082-48.36918.4685-60.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A99 - 112
2X-RAY DIFFRACTION2A113 - 135
3X-RAY DIFFRACTION3A136 - 142
4X-RAY DIFFRACTION4A143 - 175
5X-RAY DIFFRACTION5A176 - 184
6X-RAY DIFFRACTION6H2 - 28
7X-RAY DIFFRACTION7H29 - 63
8X-RAY DIFFRACTION8H64 - 118
9X-RAY DIFFRACTION9H119 - 179
10X-RAY DIFFRACTION10H180 - 216
11X-RAY DIFFRACTION11L1 - 101
12X-RAY DIFFRACTION12L102 - 114
13X-RAY DIFFRACTION13L115 - 159
14X-RAY DIFFRACTION14L160 - 177
15X-RAY DIFFRACTION15L178 - 219

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