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- PDB-7ck5: Solution structure of 28 amino acid polypeptide (354-381) in Plan... -

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Basic information

Entry
Database: PDB / ID: 7ck5
TitleSolution structure of 28 amino acid polypeptide (354-381) in Plantago asiatica mosaic virus replicase bound to SDS micelle
ComponentsPlAMV replicase peptide from RNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN / Replicase / Methyltransferase
Function / homology
Function and homology information


mRNA methyltransferase activity / RNA processing / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. ...Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPlantago asiatica mosaic potexvirus
MethodSOLUTION NMR / simulated annealing
AuthorsKomatsu, K. / Sasaki, N. / Yoshida, T. / Suzuki, K. / Masujima, Y. / Hashimoto, M. / Watanabe, S. / Tochio, N. / Kigawa, T. / Yamaji, Y. ...Komatsu, K. / Sasaki, N. / Yoshida, T. / Suzuki, K. / Masujima, Y. / Hashimoto, M. / Watanabe, S. / Tochio, N. / Kigawa, T. / Yamaji, Y. / Oshima, K. / Namba, S. / Nelson, R. / Arie, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Virol. / Year: 2021
Title: Identification of a Proline-Kinked Amphipathic alpha-Helix Downstream from the Methyltransferase Domain of a Potexvirus Replicase and Its Role in Virus Replication and Perinuclear Complex Formation.
Authors: Komatsu, K. / Sasaki, N. / Yoshida, T. / Suzuki, K. / Masujima, Y. / Hashimoto, M. / Watanabe, S. / Tochio, N. / Kigawa, T. / Yamaji, Y. / Oshima, K. / Namba, S. / Nelson, R.S. / Arie, T.
History
DepositionJul 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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

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Assembly

Deposited unit
A: PlAMV replicase peptide from RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)3,2971
Polymers3,2971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PlAMV replicase peptide from RNA-dependent RNA polymerase


Mass: 3296.862 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plantago asiatica mosaic potexvirus / Description: Cell free expression system / Gene: RdRp / Production host: Escherichia coli (E. coli) / References: UniProt: B1B578

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1161isotropic13D 1H-15N NOESY
1281isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: micelle
Contents: 1 mM [U-13C; U-15N] PlAMV replicase peptide, 20 mM [U-2H] sodium acetate, 100 mM [U-2H] SDS, 10 % [U-2H] D2O, 90% H2O/10% D2O
Label: 13C15N_peptide / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPlAMV replicase peptide[U-13C; U-15N]1
20 mMsodium acetate[U-2H]1
100 mMSDS[U-2H]1
10 %D2O[U-2H]1
Sample conditionsIonic strength: 120 mM / Label: condition_1 / pH: 5.6 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
MagRO-NMRViewKobayashi N.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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