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- PDB-8gqo: Solution NMR structure of vaccinia virus protein A28: an entry-fu... -

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Basic information

Entry
Database: PDB / ID: 8gqo
TitleSolution NMR structure of vaccinia virus protein A28: an entry-fusion complex component
ComponentsEnvelope protein A28
KeywordsVIRAL PROTEIN / Entry-fusion Complex / Cell Membrane Fusion / Vaccinia Virus
Function / homologyPoxvirus A28 / Poxvirus A28 family / viral process / viral envelope / virion membrane / membrane / Envelope protein OPG155
Function and homology information
Biological speciesVaccinia virus
MethodSOLUTION NMR / molecular dynamics
AuthorsTsai, M.H. / Wu, D.N. / Tzou, D.L.M.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 111-2113-M-001-014 Taiwan
CitationJournal: Plos Pathog. / Year: 2023
Title: Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations.
Authors: Kao, C.F. / Tsai, M.H. / Carillo, K.J. / Tzou, D.L. / Chang, W.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 14, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

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Assembly

Deposited unit
A: Envelope protein A28


Theoretical massNumber of molelcules
Total (without water)13,7241
Polymers13,7241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Envelope protein A28 / IMV MP/virus entry protein / IMV membrane protein / Integral component of the virus entry-fusion ...IMV MP/virus entry protein / IMV membrane protein / Integral component of the virus entry-fusion complex / Integral component of the virus entry/fusion complex / Integral component of virus entry/fusion complex protein / Putative signal peptide


Mass: 13724.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: WR (western reserve)
Gene: A28L, VACV_BRZ_SERRO2_149, VACV_CTGV_ALEH2_151, VACV_CTGV_CG04_151, VACV_CTGV_MI233-151, VACV_CTGV_VI04_151, 44/47.1_rMVA_142, 51.1rMVA_164, 51.2rMVA_149, IKMOJFFE_00136, List144, LIVPclone14_ ...Gene: A28L, VACV_BRZ_SERRO2_149, VACV_CTGV_ALEH2_151, VACV_CTGV_CG04_151, VACV_CTGV_MI233-151, VACV_CTGV_VI04_151, 44/47.1_rMVA_142, 51.1rMVA_164, 51.2rMVA_149, IKMOJFFE_00136, List144, LIVPclone14_158, VAC_IHDW1_152, VAC_TKT3_141, VAC_TKT4_141, VACV_CTGV_CM01_151, VACV_IOC_B141_176, Vv.00g001400
Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A4GDK2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D (H)CCH-TOCSY
181isotropic13D C(CO)NH
191isotropic13D H(CCO)NH
1101isotropic13D HBHA(CO)NH
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY
1131isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution / Contents: 50 mM sodium chloride, 50 mM MES, 90% H2O/10% D2O / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
50 mMMESnatural abundance1
Sample conditionsIonic strength: 50 NaCl mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIH3.4Schwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJ9.2.0One Moon Scientific Incorporationchemical shift assignment
NMRViewJ9.2.0One Moon Scientific Incorporationpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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