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- PDB-2m4g: Solution structure of the Core Domain (11-85) of the Murine Norov... -

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Basic information

Entry
Database: PDB / ID: 2m4g
TitleSolution structure of the Core Domain (11-85) of the Murine Norovirus VPg protein
ComponentsMurine Norovirus VPg protein
KeywordsVIRAL PROTEIN / VPg / NS5
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #70 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Arc Repressor Mutant, subunit A / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus ...Arc Repressor Mutant, subunit A - #70 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Arc Repressor Mutant, subunit A / 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 / Helix non-globular / Special / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodSOLUTION NMR / simulated annealing
AuthorsLeen, E.N. / Kwok, R. / Birtley, J.R. / Prater, S.N. / Simpson, P.J. / Matthews, S. / Marchant, J. / Curry, S.
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 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Murine Norovirus VPg protein


Theoretical massNumber of molelcules
Total (without water)8,8771
Polymers8,8771
Non-polymers00
Water00
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 Murine Norovirus VPg protein


Mass: 8876.777 Da / Num. of mol.: 1 / Fragment: Core Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Gene: VPg / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / Variant (production host): Rosetta / References: UniProt: Q80J95

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2223D (H)CCH-TOCSY
2322D 1H-13C HSQC aliphatic
2423D (H)CCH-TOCSY
2522D 1H-13C HSQC aromatic
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNCO
1913D HN(CA)CO
11013D H(CC)(CO)NH
11113D (H)C(CCO)NH
21223D (HB)CB(CGCD)HD
21323D (HB)CB(CGCDCE)HE
11413D HBHA(CBCACO)NH
21523D 1H-13C NOESY
11613D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1590 uM [U-98% 13C; U-98% 15N] MNV VPg 11-85, 50 mM sodium phosphate, 300 mM Sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
2710 uM [U-98% 13C; U-98% 15N] MNV VPg 11-85, 360 mM sodium chloride, 0.001 w/v sodium azide, 1 mM DTT, 60 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
590 uMMNV VPg 11-85-1[U-98% 13C; U-98% 15N]1
50 mMsodium phosphate-21
300 mMSodium chloride-31
1 mMDTT-41
710 uMMNV VPg 11-85-5[U-98% 13C; U-98% 15N]2
360 mMsodium chloride-62
0.001 w/vsodium azide-72
1 mMDTT-82
60 mMsodium phosphate-92
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 6.5 ambient 303 K
2360 6.5 Ambient 303 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
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
ARIALinge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
MARSZweckstetter et al., 2004chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1176 / NOE intraresidue total count: 262 / NOE long range total count: 110 / NOE medium range total count: 140 / NOE sequential total count: 106
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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