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- PDB-5ush: Structure of vaccinia virus D8 protein bound to human Fab vv66 -

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Basic information

Entry
Database: PDB / ID: 5ush
TitleStructure of vaccinia virus D8 protein bound to human Fab vv66
Components
  • Fab vv66 heavy chain
  • Fab vv66 light chain
  • IMV membrane protein
KeywordsVIRAL PROTEIN/Immune system / viral protein / antibody / Fab / Immune response / Ig fold / VIRAL PROTEIN-Immune system 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 / Roll / Immunoglobulins ...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 / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cell surface-binding protein OPG105
Similarity search - Component
Biological speciesVaccinia virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZajonc, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HHSN272200900048C United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8.
Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, ...Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, B. / Hsieh-Wilson, L.C. / Crowe, J.E. / Zajonc, D.M.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMV membrane protein
D: Fab vv66 heavy chain
E: Fab vv66 light chain
H: Fab vv66 heavy chain
L: Fab vv66 light chain
X: IMV membrane protein


Theoretical massNumber of molelcules
Total (without water)148,7366
Polymers148,7366
Non-polymers00
Water3,135174
1
A: IMV membrane protein
D: Fab vv66 heavy chain
E: Fab vv66 light chain


Theoretical massNumber of molelcules
Total (without water)74,3683
Polymers74,3683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-25 kcal/mol
Surface area27610 Å2
MethodPISA
2
H: Fab vv66 heavy chain
L: Fab vv66 light chain
X: IMV membrane protein


Theoretical massNumber of molelcules
Total (without water)74,3683
Polymers74,3683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-25 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.857, 61.515, 444.405
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 IMV membrane protein


Mass: 27965.414 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235
Source method: isolated from a genetically manipulated source
Details: CAH domain / Source: (gene. exp.) Vaccinia virus / Gene: VAC_DPP17_124, VACAC2_124, VACCL3_124 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1M1K6
#2: Antibody Fab vv66 heavy chain


Mass: 24071.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody Fab vv66 light chain


Mass: 22331.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 200 mM sodium malonate

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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: Mar 19, 2014
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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.23→38.76 Å / Num. obs: 75859 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Net I/σ(I): 15.7
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10614 / Rpim(I) all: 0.405 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E9O, 4FQQ

4e9o

4fqq


Resolution: 2.3→38.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.504 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25699 3518 5 %RANDOM
Rwork0.21817 ---
obs0.22015 66196 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.65 Å2
Refinement stepCycle: 1 / Resolution: 2.3→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 0 174 10202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910298
X-RAY DIFFRACTIONr_bond_other_d0.0010.029121
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9514060
X-RAY DIFFRACTIONr_angle_other_deg0.878321281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61151297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72824.587412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.574151576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8021527
X-RAY DIFFRACTIONr_chiral_restr0.070.21587
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022031
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_it0.5152.8465218
X-RAY DIFFRACTIONr_mcbond_other0.5152.8465217
X-RAY DIFFRACTIONr_mcangle_it0.9114.2676505
X-RAY DIFFRACTIONr_mcangle_other0.9114.2676506
X-RAY DIFFRACTIONr_scbond_it0.4332.8575080
X-RAY DIFFRACTIONr_scbond_other0.4332.8575081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7564.2717556
X-RAY DIFFRACTIONr_long_range_B_refined2.04431.81910472
X-RAY DIFFRACTIONr_long_range_B_other2.02631.76510457
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
Rfree0.385 260 -
Rwork0.344 4809 -
obs--99.92 %
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)
11.78390.01930.94551.5004-0.50824.8322-0.1054-0.4727-0.13490.28570.03610.07540.2551-0.13910.06930.5420.14950.19260.51750.12080.141910.9585-9.4517109.4244
21.5957-0.1785-0.55591.39740.40485.6354-0.06370.01880.0108-0.03570.1741-0.0630.16090.4635-0.11040.0101-0.00350.00650.1835-0.00530.0540.1945-27.02252.1295
32.7298-0.4468-0.80050.7299-0.36466.0764-0.1248-0.1703-0.18160.0140.0114-0.10990.53160.47210.11340.40830.1190.11010.14570.07150.152418.9426-10.619674.04
40.4286-0.2758-0.09531.966-0.35497.6325-0.0593-0.1886-0.2629-0.03640.02790.14510.97960.84760.03140.16650.2127-0.0020.36780.02970.19721.3108-33.29937.942
52.987-0.511-0.03735.01490.55162.5554-0.19770.07490.3350.1320.1129-0.0910.12260.22130.08470.10810.0538-0.01030.1826-0.02650.05826.39984.601947.2058
65.28222.45110.71963.9498-0.47642.21910.1709-0.12610.3780.0182-0.23940.6450.414-0.03150.06840.42750.0359-0.00030.1222-0.09070.1382-15.8335-38.868862.725
71.8016-0.9940.83122.8558-1.01713.6287-0.0953-0.0712-0.09640.0791-0.0440.22330.0379-0.21240.13920.3135-0.01190.09870.1289-0.05010.1125-0.4709-2.335871.0166
82.748-1.0714-1.30072.17711.14726.46520.0065-0.04970.06730.01730.1617-0.1088-0.58480.456-0.16820.1063-0.0482-0.00440.1232-0.04930.0521-5.6815-13.013940.1154
94.7641-0.6549-1.86452.2291-0.02583.10550.0480.095-0.02940.0253-0.13490.18350.1285-0.12350.08690.0955-0.00890.00110.1335-0.07190.058314.79212.567835.0779
104.16670.6275-0.97976.7231-2.35333.15430.2326-0.30130.52410.1978-0.06970.18190.1162-0.0343-0.16290.2588-0.04630.07670.2599-0.18410.165-14.5457-27.552575.1841
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 234
2X-RAY DIFFRACTION2X2 - 235
3X-RAY DIFFRACTION3D2 - 122
4X-RAY DIFFRACTION4H2 - 122
5X-RAY DIFFRACTION5D123 - 224
6X-RAY DIFFRACTION6H123 - 222
7X-RAY DIFFRACTION7E2 - 112
8X-RAY DIFFRACTION8L2 - 112
9X-RAY DIFFRACTION9E113 - 213
10X-RAY DIFFRACTION10L113 - 213

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