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- PDB-5x5w: Crystal structure of pseudorabies virus glycoprotein D -

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Basic information

Entry
Database: PDB / ID: 5x5w
TitleCrystal structure of pseudorabies virus glycoprotein D
Components
  • GD
  • Nectin-1Poliovirus receptor-related 1
KeywordsVIRAL PROTEIN/CELL ADHESION / herpes simplex virus / pseudorabies virus / glycoprotein D / VIRAL PROTEIN-CELL ADHESION complex
Function / homology
Function and homology information


protein localization to cell junction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / positive regulation of viral entry into host cell / membrane => GO:0016020 / synapse / virion attachment to host cell ...protein localization to cell junction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / positive regulation of viral entry into host cell / membrane => GO:0016020 / synapse / virion attachment to host cell / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nectin-1 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Nectin-1 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSuid herpesvirus 1
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: To Be Published
Title: Crystal structure of pseudorabies virus glycoprotein D
Authors: Li, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GD
B: Nectin-1
C: GD
D: Nectin-1


Theoretical massNumber of molelcules
Total (without water)112,9714
Polymers112,9714
Non-polymers00
Water1,53185
1
A: GD
B: Nectin-1


Theoretical massNumber of molelcules
Total (without water)56,4852
Polymers56,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-14 kcal/mol
Surface area15860 Å2
MethodPISA
2
C: GD
D: Nectin-1


Theoretical massNumber of molelcules
Total (without water)56,4852
Polymers56,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.945, 98.110, 128.395
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 GD / glycoprotein D


Mass: 44584.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Strain: Becker / Gene: US6 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G3G933
#2: Protein Nectin-1 / Poliovirus receptor-related 1 / Herpes virus entry mediator C / HveC / Nectin cell adhesion molecule 1 / Poliovirus receptor-related protein 1


Mass: 11900.503 Da / Num. of mol.: 2 / Fragment: UNP residues 37-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: NECTIN1, HVEC, PRR1, PVRL1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9GL76
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M sodium chloride, 0.1M sodium acetate pH 5.5, 20% w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28419 / % possible obs: 99.9 % / Redundancy: 8.6 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.7→2.8 Å / CC1/2: 0.828 / Rpim(I) all: 0.419

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U82

3u82


Resolution: 2.7→38.166 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8
RfactorNum. reflection% reflection
Rfree0.2664 1426 5.05 %
Rwork0.2379 --
obs0.2393 28251 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 0 85 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155637
X-RAY DIFFRACTIONf_angle_d1.5127691
X-RAY DIFFRACTIONf_dihedral_angle_d17.7462049
X-RAY DIFFRACTIONf_chiral_restr0.09815
X-RAY DIFFRACTIONf_plane_restr0.0091009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6966-2.79290.4061420.35292519X-RAY DIFFRACTION96
2.7929-2.90470.35511400.31872647X-RAY DIFFRACTION99
2.9047-3.03690.3421480.29132645X-RAY DIFFRACTION100
3.0369-3.19690.33771380.28682662X-RAY DIFFRACTION99
3.1969-3.39710.25351320.25672675X-RAY DIFFRACTION100
3.3971-3.65920.28691470.23222693X-RAY DIFFRACTION100
3.6592-4.02710.23011380.2112689X-RAY DIFFRACTION100
4.0271-4.60890.20431570.18812698X-RAY DIFFRACTION100
4.6089-5.80350.23351620.19352730X-RAY DIFFRACTION100
5.8035-38.16950.23961220.23152867X-RAY DIFFRACTION99
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)
12.0211-0.15790.35781.51110.35832.0732-0.01840.25540.0666-0.0856-0.00480.0471-0.1396-0.2840.03940.1858-0.0083-0.01380.24750.01830.1712103.8179106.7552120.4749
21.3077-0.6490.14732.1854-0.76952.5174-0.1946-0.29880.03-0.02490.1453-0.079-0.0569-0.05580.01910.3123-0.0459-0.04320.39220.01820.2841111.8148105.167145.6428
32.78540.15360.37751.17170.18761.9223-0.0405-0.3846-0.1040.07280.01790.04570.2201-0.06570.03660.21790.00670.03220.26690.02610.181863.816888.8082120.4766
41.88490.6258-0.01811.9543-0.58492.333-0.1260.09470.0745-0.12590.0067-0.0470.14050.15350.03010.30160.04510.03280.3032-0.01850.271171.622991.145395.3368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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