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- PDB-2mxd: Solution structure of VPg of porcine sapovirus -

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Basic information

Entry
Database: PDB / ID: 2mxd
TitleSolution structure of VPg of porcine sapovirus
ComponentsViral protein genome-linked
KeywordsVIRAL PROTEIN / Viral protein genome-linked / Porcine sapovirus
Function / homology
Function and homology information


calicivirin / RNA-protein covalent cross-linking / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / RNA-protein covalent cross-linking / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #110 / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / 434 Repressor (Amino-terminal Domain) / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...434 Repressor (Amino-terminal Domain) - #110 / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / 434 Repressor (Amino-terminal Domain) / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPorcine enteric sapovirus
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsKim, J. / Hwang, H. / Min, H. / Yun, H. / Cho, K. / Pelton, J.G. / Wemmer, D.E. / Lee, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch.
Authors: Hwang, H.J. / Min, H.J. / Yun, H. / Pelton, J.G. / Wemmer, D.E. / Cho, K.O. / Kim, J.S. / Lee, C.W.
History
DepositionDec 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral protein genome-linked


Theoretical massNumber of molelcules
Total (without water)7,3821
Polymers7,3821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Viral protein genome-linked / / VPg


Mass: 7382.227 Da / Num. of mol.: 1 / Fragment: UNP residues 948-1006
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine enteric sapovirus / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QEJ5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D (H)CCH-COSY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] protein, 10 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 13C; U-99% 15N]1
10 mMpotassium phosphate-21
Sample conditionsIonic strength: 10 / pH: 6.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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