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- PDB-2mmi: Mengovirus Leader: Structural Characterization of the Mengovirus ... -

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Basic information

Entry
Database: PDB / ID: 2mmi
TitleMengovirus Leader: Structural Characterization of the Mengovirus Leader Protein Bound to Ran GTPase by Nuclear Magnetic Resonance
ComponentsLeader proteinLeadership
KeywordsVIRAL PROTEIN / animal viruses / positive-strand RNA viruses / cardioviruses / leader / nucleocytoplasmic transport
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 / : / protein complex oligomerization / monoatomic ion channel activity / 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 / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / 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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral ...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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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. / Cornilescu, C.C. / Markley, J.L. / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)8,3272
Polymers8,2621
Non-polymers651
Water0
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 / Leadership


Mass: 8262.046 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

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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, 0.5 mM Ran GTPase, 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-1[U-100% 13C; U-100% 15N]1
0.5 mMRan GTPase-21
20 mMHEPES-31
100 mMpotassium chloride-41
2 mMmagnesium chloride-51
2 mMDTT-61
0.04 %sodium azide-71
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
SparkyGoddardchemical shift assignment
SPARTA+Shen and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
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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