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- PDB-2lnc: Solution NMR structure of Norwalk virus protease -

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Basic information

Entry
Database: PDB / ID: 2lnc
TitleSolution NMR structure of Norwalk virus protease
Components3C-like protease
KeywordsHYDROLASE / Viral Protease / Chymotrypsin-like protease / Calicivirus
Function / homology
Function and homology information


calicivirin / host cell membrane / 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 ...calicivirin / host cell membrane / 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 / membrane
Similarity search - Function
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 / 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 / Trypsin-like serine proteases ...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 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTakahashi, D. / Hiromasa, Y. / Kim, Y. / Anbanandam, A. / Chang, K. / Prakash, O.
CitationJournal: Protein Sci. / Year: 2013
Title: Structural and dynamics characterization of norovirus protease.
Authors: Takahashi, D. / Hiromasa, Y. / Kim, Y. / Anbanandam, A. / Yao, X. / Chang, K.O. / Prakash, O.
History
DepositionDec 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)20,1261
Polymers20,1261
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 #1lowest energy

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Components

#1: Protein 3C-like protease / 3CLpro


Mass: 20126.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83883, calicivirin

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1422D 1H-15N HSQC
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1813D HN(CA)CO
1913D HN(CA)CB
11013D CBCA(CO)NH
11113D C(CO)NH
11213D H(CCO)NH
11313D 1H-15N NOESY
11413D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] Norovirus protease, 50 mM sodium phosphate, 100 mM sodium chloride, 3 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 15N] Norovirus protease, 50 mM sodium phosphate, 100 mM sodium chloride, 3 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMNorovirus protease-1[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
3 mMsodium azide-41
0.5 mMNorovirus protease-5[U-99% 15N]2
50 mMsodium phosphate-62
100 mMsodium chloride-72
3 mMsodium azide-82
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian UnityPlusVarianUNITYPLUS5002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2650 / NOE intraresidue total count: 515 / NOE long range total count: 825 / NOE medium range total count: 329 / NOE sequential total count: 981 / Protein phi angle constraints total count: 98 / Protein psi angle constraints total count: 100
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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