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- PDB-5zs0: Structure of glycoprotein B Domain IV of pseudorabies virus with ... -

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Basic information

Entry
Database: PDB / ID: 5zs0
TitleStructure of glycoprotein B Domain IV of pseudorabies virus with 7B11 antibody
Components
  • 7B11 heavy chain
  • 7B11 light chain
  • Envelope glycoprotein B,Envelope glycoprotein B
KeywordsVIRAL PROTEIN / complex with antibody / fusion protein
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
SH3 type barrels. - #1230 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / SH3 type barrels. / Roll ...SH3 type barrels. - #1230 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / SH3 type barrels. / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B / Envelope glycoprotein B
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsHu, X.L. / Yang, F.L.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structural Basis for the Recognition of Pseudorabies Virus Glycoprotein B by a Complement-dependent Neutralizing Antibody
Authors: Hu, X.L. / Peng, R.C. / Li, X.D.
History
DepositionApr 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7B11 light chain
B: 7B11 heavy chain
C: Envelope glycoprotein B,Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)74,4213
Polymers74,4213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-22 kcal/mol
Surface area30320 Å2
Unit cell
Length a, b, c (Å)128.907, 128.907, 194.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Antibody 7B11 light chain


Mass: 23274.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody 7B11 heavy chain


Mass: 23548.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Envelope glycoprotein B,Envelope glycoprotein B / gB / gB


Mass: 27597.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid alphaherpesvirus 1 / Gene: gB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0U3FH21, UniProt: A0A1Q0AKY5

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium phosphate dibasic and 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 14967 / % possible obs: 99.8 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 21.35
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 2.696 / Rsym value: 2.696

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YS2

5ys2


Resolution: 3.29→50 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.796 / SU B: 30.436 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.697 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3097 559 4.5 %RANDOM
Rwork0.24072 ---
obs0.2439 12295 80.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 3.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 0 0 4628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194728
X-RAY DIFFRACTIONr_bond_other_d0.0020.024241
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9476423
X-RAY DIFFRACTIONr_angle_other_deg1.04139849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4595596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64223.433201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.44315756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0861534
X-RAY DIFFRACTIONr_chiral_restr0.0890.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215263
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
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_it3.5916.4262402
X-RAY DIFFRACTIONr_mcbond_other3.5766.4252401
X-RAY DIFFRACTIONr_mcangle_it6.0959.6172992
X-RAY DIFFRACTIONr_mcangle_other6.0969.6192993
X-RAY DIFFRACTIONr_scbond_it3.0446.6812326
X-RAY DIFFRACTIONr_scbond_other3.0436.6832327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3119.9143432
X-RAY DIFFRACTIONr_long_range_B_refined9.96974.3885141
X-RAY DIFFRACTIONr_long_range_B_other9.9774.4075142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.288→3.373 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 7 -
Rwork0.309 117 -
obs--11.58 %

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