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- PDB-8osq: Why does the herpes simplex 1 virus-encoded UL49.5 protein fail t... -

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Basic information

Entry
Database: PDB / ID: 8osq
TitleWhy does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation?
ComponentsEnvelope glycoprotein N
KeywordsVIRAL PROTEIN / UL49.5 protein / HSV-1 / herpesvirus / molecular dynamics / ER membrane
Function / homologyHerpesvirus UL49A / Envelope glycoprotein N / host cell membrane / host cell Golgi apparatus / viral envelope / virion membrane / membrane / Envelope glycoprotein N
Function and homology information
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
MethodSOLUTION NMR / molecular dynamics
AuthorsZhukov, I. / Krupa, P. / Karska, N. / Rodziewicz-Motowidlo, S. / Lipinska, A.D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/04/X/ST4/01491 Poland
CitationJournal: To Be Published
Title: Why doesn't the UL49.5 protein from HSV-1 virus inhibit the TAP antigen presentation pathway?
Authors: Karska, N. / Zhukov, I. / Lipinska, A.D. / Rodziewicz-Motowidlo, S. / Krupa, P.
History
DepositionApr 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein N


Theoretical massNumber of molelcules
Total (without water)3,3801
Polymers3,3801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Envelope glycoprotein N


Mass: 3379.504 Da / Num. of mol.: 1 / Mutation: C46ABU M54NLE / Source method: obtained synthetically
Source: (synth.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: O09800
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic22D 1H-1H NOESY
141isotropic22D 1H-1H TOCSY
151isotropic22D 1H-1H ROESY

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Sample preparation

DetailsType: micelle / Contents: 0.4 mM NA- NHSV, 90% H2O/10% D2O / Label: sample 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.4 mM / Component: NHSV / Isotopic labeling: NA-
Sample conditionsIonic strength: 50 mM / Ionic strength err: 5 / Label: conditions_1 / pH: 7.5 / PH err: 0.2 / Pressure: 1 bar / Temperature: 303 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.3Agilent Inc.collection
TopSpin3.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: 243 restraints were used
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 20

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