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- PDB-5ys6: Structure of the ectodomain of pseudorabies virus glycoproten B -

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Basic information

Entry
Database: PDB / ID: 5ys6
TitleStructure of the ectodomain of pseudorabies virus glycoproten B
ComponentsPRV glycoproten B
KeywordsVIRAL PROTEIN / fusion glycoprotein
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / 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 / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein B / Envelope glycoprotein B
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHu, X.L. / Yang, F.L.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Two classes of protective antibodies against pseudorabies virus variant glycoprotein B: implications for vaccine design
Authors: Li, X.D. / Yang, F.L. / Hu, X.L.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 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: PRV glycoproten B


Theoretical massNumber of molelcules
Total (without water)78,4581
Polymers78,4581
Non-polymers00
Water0
1
A: PRV glycoproten B

A: PRV glycoproten B

A: PRV glycoproten B


Theoretical massNumber of molelcules
Total (without water)235,3733
Polymers235,3733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area33440 Å2
ΔGint-170 kcal/mol
Surface area81320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.288, 100.288, 272.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PRV glycoproten B / Envelope glycoprotein B / gB


Mass: 78457.734 Da / Num. of mol.: 1 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid alphaherpesvirus 1 / Gene: gB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1Q0AKY3, UniProt: T2FL65*PLUS

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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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 34% PEG 200, 0.1 M citric acid

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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: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 18750 / % possible obs: 99.9 % / Redundancy: 5.1 % / Net I/σ(I): 15.779
Reflection shellResolution: 3.1→3.21 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUM

2gum


Resolution: 3.1→35.569 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.2667 958 5.12 %
Rwork0.2271 --
obs0.229 18723 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→35.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 0 0 4582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064691
X-RAY DIFFRACTIONf_angle_d0.9826359
X-RAY DIFFRACTIONf_dihedral_angle_d16.4471727
X-RAY DIFFRACTIONf_chiral_restr0.039691
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0891-3.25190.37461660.3322492X-RAY DIFFRACTION99
3.2519-3.45550.35171390.28732547X-RAY DIFFRACTION100
3.4555-3.7220.33331510.25752532X-RAY DIFFRACTION100
3.722-4.09610.30161380.24362515X-RAY DIFFRACTION100
4.0961-4.68760.23891130.19842581X-RAY DIFFRACTION100
4.6876-5.90150.24711330.21612543X-RAY DIFFRACTION100
5.9015-35.57120.2011180.1982555X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 93.7403 Å / Origin y: 55.2084 Å / Origin z: 25.0454 Å
111213212223313233
T0.3091 Å2-0.0412 Å20.0256 Å2-0.3724 Å2-0.0181 Å2--0.4394 Å2
L0.391 °2-0.0731 °2-0.2566 °2-0.3464 °2-0.0637 °2--0.3916 °2
S-0.1041 Å °-0.0517 Å °-0.0112 Å °0.08 Å °-0.0189 Å °0.0354 Å °0.0741 Å °0.0202 Å °-0 Å °
Refinement TLS groupSelection details: all

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