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- PDB-6tm8: Crystal structure of glycoprotein D of Equine Herpesvirus Type 4 -

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Basic information

Entry
Database: PDB / ID: 6tm8
TitleCrystal structure of glycoprotein D of Equine Herpesvirus Type 4
ComponentsEnvelope glycoprotein D
KeywordsVIRAL PROTEIN / glycoprotein D / equine herpesvirus type 4 / EHV-4 / viral entry
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / membrane => GO:0016020 / Immunoglobulin-like domain superfamily / viral envelope / Envelope glycoprotein D
Function and homology information
Biological speciesEquid alphaherpesvirus 4 (Equine herpesvirus 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKremling, V. / Loll, B. / Osterrieder, N. / Wahl, M. / Dahmani, I. / Chiantia, P. / Azab, W.
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
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3925
Polymers38,0241
Non-polymers3684
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-1 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.095, 59.554, 69.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Envelope glycoprotein D


Mass: 38023.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equid alphaherpesvirus 4 (Equine herpesvirus 4)
Gene: ORF72 / Plasmid: pMultiBac / Cell line (production host): H5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0A4Z5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM MgCl2, 100 mM MES pH 6.5, 30% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23671 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.174 / Net I/σ(I): 8.96
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.5 % / Num. unique obs: 10835 / CC1/2: 0.409 / Rrim(I) all: 1.268 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SQJ

6sqj


Resolution: 1.9→46.17 Å / SU ML: 0.2323 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9286
RfactorNum. reflection% reflection
Rfree0.2131 1181 5 %
Rwork0.1747 --
obs0.1766 23641 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 24 174 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182116
X-RAY DIFFRACTIONf_angle_d1.04842882
X-RAY DIFFRACTIONf_chiral_restr0.0724312
X-RAY DIFFRACTIONf_plane_restr0.0062376
X-RAY DIFFRACTIONf_dihedral_angle_d15.70341281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.36221150.2892209X-RAY DIFFRACTION76.1
1.98-2.090.25911380.2392610X-RAY DIFFRACTION90.96
2.09-2.220.24721510.21382885X-RAY DIFFRACTION99.41
2.22-2.390.24611520.18742898X-RAY DIFFRACTION99.87
2.39-2.630.22381520.18572890X-RAY DIFFRACTION99.54
2.63-3.010.21221540.17052928X-RAY DIFFRACTION99.68
3.01-3.790.20411560.15092959X-RAY DIFFRACTION99.71
3.79-46.170.17071630.15243081X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: -18.3823856533 Å / Origin y: -2.65350132849 Å / Origin z: 8.15552908134 Å
111213212223313233
T0.187538718025 Å2-0.00716998000124 Å2-0.0174305586347 Å2-0.19181688238 Å2-0.00774676326183 Å2--0.175914811394 Å2
L1.08303448248 °2-0.271478573776 °2-0.56564048638 °2-0.883928083347 °20.112895920261 °2--1.51176230378 °2
S0.00888018239749 Å °-0.0358414703727 Å °0.0771489708006 Å °0.0378010810245 Å °0.0388934891896 Å °-0.0704737126119 Å °-0.0126606984911 Å °0.076896253245 Å °-0.0440381811389 Å °
Refinement TLS groupSelection details: all

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