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- PDB-1l1n: POLIOVIRUS 3C PROTEINASE -

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Basic information

Entry
Database: PDB / ID: 1l1n
TitlePOLIOVIRUS 3C PROTEINASE
ComponentsGenome polyprotein: Picornain 3C
KeywordsViral protein / hydrolase / BETA BARREL / TRYPSIN-LIKE / CATALYTIC TRIAD
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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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) / Picornavirales 3C/3C-like protease domain ...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) / 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 / 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 speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsMosimann, S.C. / Chernaia, M.M. / Sia, S. / Plotch, S. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Refined X-ray crystallographic structure of the poliovirus 3C gene product.
Authors: Mosimann, S.C. / Cherney, M.M. / Sia, S. / Plotch, S. / James, M.N.
History
DepositionFeb 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein: Picornain 3C
B: Genome polyprotein: Picornain 3C


Theoretical massNumber of molelcules
Total (without water)39,2952
Polymers39,2952
Non-polymers00
Water2,432135
1
A: Genome polyprotein: Picornain 3C


Theoretical massNumber of molelcules
Total (without water)19,6471
Polymers19,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome polyprotein: Picornain 3C


Theoretical massNumber of molelcules
Total (without water)19,6471
Polymers19,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.260, 116.310, 47.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Genome polyprotein: Picornain 3C / Protease 3C / P3C


Mass: 19647.314 Da / Num. of mol.: 2 / Fragment: Residues 1565-1747
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / Gene: 3C / Plasmid: PT7-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03300, picornain 3C
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, glycerol, mercaptoethanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 0
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDDetails
117-20 mg/mlprotein1drop
220 %(w/v)ammonium sulfate1drop
35 mMbeta-mercaptoethanol1drop
442 %ammonium sulfate1reservoir
52 %(v/v)glycerol1reservoir
6mMbeta-mercaptoethanol1reservoirpH5.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 18, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 28160 / Num. obs: 26218 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3 / Num. unique all: 3446 / % possible all: 80.9
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 80.9 % / Num. unique obs: 3446 / Rmerge(I) obs: 0.181

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 1143 Random
Rwork0.213 --
obs-22854 -
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 0 135 2822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.8
Refinement
*PLUS
Rfactor obs: 0.213 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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