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- PDB-6esc: Crystal structure of Pseudorabies virus glycoprotein B -

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Basic information

Entry
Database: PDB / ID: 6esc
TitleCrystal structure of Pseudorabies virus glycoprotein B
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / herpesvirus / fusion protein / class III / viral entry
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
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
Similarity search - Component
Biological speciesSuid alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBackovic, M. / Vaney, M.C. / Rey, F.A. / Haouz, A.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: J.Virol. / Year: 2018
Title: Structure-Function Dissection of Pseudorabies Virus Glycoprotein B Fusion Loops.
Authors: Vallbracht, M. / Brun, D. / Tassinari, M. / Vaney, M.C. / Pehau-Arnaudet, G. / Guardado-Calvo, P. / Haouz, A. / Klupp, B.G. / Mettenleiter, T.C. / Rey, F.A. / Backovic, M.
History
DepositionOct 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5433
Polymers82,2301
Non-polymers3132
Water1,65792
1
A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,6299
Polymers246,6893
Non-polymers9406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38460 Å2
ΔGint-142 kcal/mol
Surface area80510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.890, 99.890, 272.800
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 Envelope glycoprotein B / gB


Mass: 82229.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid alphaherpesvirus 1 / Gene: UL27, gB / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's Drosophila Line 2 / References: UniProt: G3G8X1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.19 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 7% PEG 4,000, 0.6M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2015 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.69→46.15 Å / Num. obs: 28086 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 86.38 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.055 / Net I/σ(I): 14.99
Reflection shellResolution: 2.69→2.85 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.33 / CC1/2: 0.82 / Rpim(I) all: 0.386 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUM

2gum


Resolution: 2.7→46.15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.366 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1385 5 %RANDOM
Rwork0.193 ---
obs0.195 27695 99.4 %-
Displacement parametersBiso mean: 73.49 Å2
Baniso -1Baniso -2Baniso -3
1--10.04 Å20 Å20 Å2
2---10.04 Å20 Å2
3---20.0799 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.7→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 20 92 4875
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014894HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.176645HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1704SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes731HARMONIC5
X-RAY DIFFRACTIONt_it4894HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion19.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion629SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5194SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3685 137 5 %
Rwork0.2817 2601 -
all0.286 2738 -
obs--94.61 %

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