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- PDB-6sqj: Crystal structure of glycoprotein D of Equine Herpesvirus Type 1 -

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Basic information

Entry
Database: PDB / ID: 6sqj
TitleCrystal structure of glycoprotein D of Equine Herpesvirus Type 1
ComponentsGlycoprotein D
KeywordsVIRAL PROTEIN / glycoprotein D / equine herpesvirus type 1 / viral entry
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like domain superfamily / viral envelope / membrane / metal ion binding / Glycoprotein D / Glycoprotein D
Function and homology information
Biological speciesEquid alphaherpesvirus 1 (Equine herpesvirus 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.245 Å
AuthorsKremling, V. / Loll, B. / Azab, W. / Osterrieder, N. / Dahmani, I. / Chiantia, P. / Wahl, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Front Microbiol / Year: 2023
Title: Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I.
Authors: Kremling, V. / Loll, B. / Pach, S. / Dahmani, I. / Weise, C. / Wolber, G. / Chiantia, S. / Wahl, M.C. / Osterrieder, N. / Azab, W.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein D
B: Glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1017
Polymers75,9822
Non-polymers1,1195
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-12 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.860, 94.464, 101.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoprotein D


Mass: 37990.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equid alphaherpesvirus 1 (Equine herpesvirus 1)
Plasmid: pMultiBacY / Cell line (production host): H5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G9HV37, UniProt: Q04245*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris buffer, 0.2 M magnesium chloride, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 33402 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 11.71
Reflection shellResolution: 2.24→2.38 Å / Num. unique obs: 5140 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C36

2c36


Resolution: 2.245→49.803 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.73
RfactorNum. reflection% reflection
Rfree0.2574 1669 5 %
Rwork0.2033 --
obs0.206 33379 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.78 Å2 / Biso mean: 58.7663 Å2 / Biso min: 30.46 Å2
Refinement stepCycle: final / Resolution: 2.245→49.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 72 132 4002
Biso mean--106.68 53.46 -
Num. residues----472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.31070.35491300.343245594
2.3107-2.38530.34931360.317258599
2.3853-2.47050.39221380.28682634100
2.4705-2.56940.34181380.28552611100
2.5694-2.68640.32171380.26352620100
2.6864-2.8280.30751390.24052645100
2.828-3.00520.32321380.23622630100
3.0052-3.23710.30231400.23272645100
3.2371-3.56280.25031400.20242664100
3.5628-4.07820.26041410.17722682100
4.0782-5.13720.17671430.14512718100
5.1372-49.80.22221480.18052821100

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