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- PDB-2mml: T47 phosphorylation of the Mengovirus Leader Protein: NMR Studies... -

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Basic information

Entry
Database: PDB / ID: 2mml
TitleT47 phosphorylation of the Mengovirus Leader Protein: NMR Studies of the Phosphorylation of the Mengovirus Leader Protein Reveal Stabilization of Intermolecular Domain Interactions
ComponentsLeader protein
KeywordsVIRAL PROTEIN / animal viruses / positive-strand RNA viruses / cardioviruses / leader / protein phosphorylation / casein kinase 2
Function / homology
Function and homology information


positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / symbiont-mediated suppression of host gene expression / channel activity / monoatomic ion transmembrane transport / RNA helicase activity ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / symbiont-mediated suppression of host gene expression / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesMengo virus
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBacot-Davis, V.R. / Porter, F.W. / Palmenberg, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Solution structures of Mengovirus Leader protein, its phosphorylated derivatives, and in complex with nuclear transport regulatory protein, RanGTPase.
Authors: Bacot-Davis, V.R. / Ciomperlik, J.J. / Basta, H.A. / Cornilescu, C.C. / Palmenberg, A.C.
History
DepositionMar 15, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leader protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4072
Polymers8,3421
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Leader protein


Mass: 8342.025 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Strain: EMCV / Plasmid: pET41B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12296
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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-13C HSQC
1313D (H)CCH-TOCSY
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11011D 31P

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] L Mengo 1P, 20 mM HEPES, 100 mM potassium chloride, 2 mM magnesium chloride, 2 mM DTT, 0.04 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mML Mengo 1P-1[U-100% 13C; U-100% 15N]1
20 mMHEPES-21
100 mMpotassium chloride-31
2 mMmagnesium chloride-41
2 mMDTT-51
0.04 %sodium azide-61
Sample conditionsIonic strength: 102 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SPARTA+Shen and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxgeometry optimization
SparkyGoddardchemical shift assignment
CARAWuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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