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- PDB-2m4h: Solution structure of the Core Domain (10-76) of the Feline Calic... -

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Basic information

Entry
Database: PDB / ID: 2m4h
TitleSolution structure of the Core Domain (10-76) of the Feline Calicivirus VPg protein
ComponentsFeline Calicivirus VPg protein
KeywordsVIRAL PROTEIN / NS5 / VPg
Function / homology
Function and homology information


calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host gene expression / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host gene expression / 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 / 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 ...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 / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesFeline calicivirus
MethodSOLUTION NMR / simulated annealing
AuthorsKwok, R.N. / Leen, E.N. / Birtley, J.R. / Prater, S.N. / Simpson, P.J. / Curry, S. / Matthews, S. / Marchant, J.
CitationJournal: J.Virol. / Year: 2013
Title: Structures of the Compact Helical Core Domains of Feline Calicivirus and Murine Norovirus VPg Proteins.
Authors: Leen, E.N. / Kwok, K.Y. / Birtley, J.R. / Simpson, P.J. / Subba-Reddy, C.V. / Chaudhry, Y. / Sosnovtsev, S.V. / Green, K.Y. / Prater, S.N. / Tong, M. / Young, J.C. / Chung, L.M. / Marchant, ...Authors: Leen, E.N. / Kwok, K.Y. / Birtley, J.R. / Simpson, P.J. / Subba-Reddy, C.V. / Chaudhry, Y. / Sosnovtsev, S.V. / Green, K.Y. / Prater, S.N. / Tong, M. / Young, J.C. / Chung, L.M. / Marchant, J. / Roberts, L.O. / Kao, C.C. / Matthews, S. / Goodfellow, I.G. / Curry, S.
History
DepositionFeb 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Oct 5, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.4May 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: Feline Calicivirus VPg protein


Theoretical massNumber of molelcules
Total (without water)8,3631
Polymers8,3631
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 #1closest to the average

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Components

#1: Protein Feline Calicivirus VPg protein


Mass: 8363.147 Da / Num. of mol.: 1 / Fragment: Core Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline calicivirus / Strain: F9 / Gene: ORF1, VPg / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P27409

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HBHA(CBCACO)NH
1613D 1H-15N NOESY
2723D (H)CCH-TOCSY
2823D 1H-13C NOESY
2922D 1H-13C HSQC aromatic
21022D 1H-13C HSQC aliphatic
31132D 1H-15N HSQC
11213D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
1100-200 uM [U-99% 13C; U-99% 15N] FCV VPg 7-76, 300 mM sodium chloride, 20 mM HEPES, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
2100-200 uM [U-99% 13C; U-99% 15N] FCV VPg 7-76, 300 mM sodium chloride, 1 mM sodium azide, 20 mM HEPES, 100% D2O100% D2O
3100-200 uM [U-99% 13C; U-99% 15N] FCV VPg 7-76, 300 mM sodium chloride, 1 mM sodium azide, 20 mM HEPES, 15 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMFCV VPg 7-76-1[U-99% 13C; U-99% 15N]100-2001
300 mMsodium chloride-21
20 mMHEPES-31
1 mMsodium azide-41
uMFCV VPg 7-76-5[U-99% 13C; U-99% 15N]100-2002
300 mMsodium chloride-62
1 mMsodium azide-72
20 mMHEPES-82
uMFCV VPg 7-76-9[U-99% 13C; U-99% 15N]100-2003
300 mMsodium chloride-103
1 mMsodium azide-113
20 mMHEPES-123
15 mg/mLPf1 phage-133
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 7.0 ambient 283 K
2300 7.0 ambient 283 K
3300 7.0 Ambient 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxgeometry optimization
ARIALinge, O'Donoghue and Nilgesstructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
MARSZweckstetter et al., 2004chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1172 / NOE intraresidue total count: 373 / NOE long range total count: 144 / NOE medium range total count: 153 / NOE sequential total count: 197
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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