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- PDB-2bbl: NMR structures of the peptide linked to the genome (VPg) of polio... -

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Entry
Database: PDB / ID: 2bbl
TitleNMR structures of the peptide linked to the genome (VPg) of poliovirus in a stabilizing solvent
ComponentsGenome linked protein VPg
KeywordsVIRAL PROTEIN / peptide primer / RNA synthesis / uridylylation / viral replication / polymerase cofactor
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Genome polyprotein
Similarity search - Component
MethodSOLUTION NMR / automatic NOE assignment in combination with distance geometry
AuthorsSchein, C.H. / Oezguen, N.
Citation
Journal: Peptides / Year: 2006
Title: NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.
Authors: Schein, C.H. / Oezguen, N. / Volk, D.E. / Garimella, R. / Paul, A. / Braun, W.
#1: Journal: Proteins / Year: 2006
Title: Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses
Authors: Schein, C.H. / Volk, D.E. / Oezguen, N. / Paul, A.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome linked protein VPg


Theoretical massNumber of molelcules
Total (without water)2,3581
Polymers2,3581
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)10 / 50target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Genome linked protein VPg


Mass: 2357.749 Da / Num. of mol.: 1 / Fragment: residues 1-22 / Source method: obtained synthetically
Details: This sequence occurs naturally in human poliovirus serotype 1.
References: GenBank: 25121847, UniProt: P03300*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
NMR detailsText: Spectra were collected at 283K

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Sample preparation

DetailsContents: VPg 2.78 mM, 0.01 M sodium phosphate buffer, pH 7.2, 4M deuterated Trimethylamine oxide, 10% D2O
Solvent system: 10%D2O
Sample conditionsIonic strength: 10mM sodium phosphate / pH: 7.2 / Pressure: atmospheric atm / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
NOAH2Mumenthaler, C. et alstructure solution
DIAMOD2.2Guentert, P. et alstructure solution
Felixdata analysis
DIAMOD2.2Guentert, P. et alrefinement
RefinementMethod: automatic NOE assignment in combination with distance geometry
Software ordinal: 1
Details: Refinement of the NOE assignment is performed iteratively. NOAH passes geometrical constraints derived from the NOE list to DIAMOD. DIAMOD calculates a bundle of structures with least ...Details: Refinement of the NOE assignment is performed iteratively. NOAH passes geometrical constraints derived from the NOE list to DIAMOD. DIAMOD calculates a bundle of structures with least violation of the constraints. The new bundle of structures is the basis for refinement of the assignments in NOAH.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 10

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