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- PDB-8wt5: Vaccinia Virus J5 ectodomain -

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Basic information

Entry
Database: PDB / ID: 8wt5
TitleVaccinia Virus J5 ectodomain
ComponentsProtein J5
KeywordsVIRAL PROTEIN / Entry Fusion Complex Protein
Function / homologyPox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / membrane / Protein J5
Function and homology information
Biological speciesVaccinia virus Western Reserve
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsCarillo, K.J. / Tzou, D.L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Solution NMR Structure of Vaccinia Virus Protein J5 (2 - 68 a.a)
Authors: Carillo, K.J. / Tzou, D.L.
History
DepositionOct 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein J5


Theoretical massNumber of molelcules
Total (without water)7,7931
Polymers7,7931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein J5


Mass: 7792.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: MVA089L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76VD9
Has protein modificationY

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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
121isotropic13D 1H-13C NOESY
131isotropic13D 1H-15N NOESY
141isotropic13D HBHA(CO)NH
151isotropic13D CBCA(CO)NH
161isotropic13D HNCA
171isotropic13D HN(CO)CA
181isotropic13D (H)CCH-COSY
191isotropic13D (H)CCH-TOCSY
1101isotropic13D HN(COCA)CB
1111isotropic13D HNCO

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] Vaccinia Virus Protein J5, 137 mM no label sodium chloride, 2.7 mM no label potassium chloride, 10 mM no label disodium phosphate, 1.8 mM no label potassium ...Contents: 0.5 mM [U-100% 13C; U-100% 15N] Vaccinia Virus Protein J5, 137 mM no label sodium chloride, 2.7 mM no label potassium chloride, 10 mM no label disodium phosphate, 1.8 mM no label potassium dihydrogen phosphate, 90% H2O/10% D2O
Details: Sample was prepared with 13C and 15N label in 1X PBS buffer pH 6.5
Label: 13C_15N_J5 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVaccinia Virus Protein J5[U-100% 13C; U-100% 15N]1
137 mMsodium chlorideno label1
2.7 mMpotassium chlorideno label1
10 mMdisodium phosphateno label1
1.8 mMpotassium dihydrogen phosphateno label1
Sample conditionsDetails: J5 protein sample was expressed with 15N and 13C label
Ionic strength: 8.1 mM / Label: 13C_15N_labeled_J5 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker BRUKER AVANCE III 600 / Manufacturer: Bruker / Model: BRUKER AVANCE III 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
TopSpin4.3.0Bruker Biospinprocessing
TopSpin4.3.0Bruker Biospincollection
X-PLOR NIH3.7Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.7Schwieters, Kuszewski, Tjandra and Clorerefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARA1.8.4Keller and Wuthrichpeak picking
Refinement
MethodSoftware ordinal
simulated annealing5
molecular dynamics6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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