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- PDB-4wyw: Mutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus -

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Basic information

Entry
Database: PDB / ID: 4wyw
TitleMutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus
ComponentsRNA-directed RNA polymerase 3D-POL
KeywordsTRANSFERASE / closed-right hand RNA dependent RNA polymerase Picornavirus
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / 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 / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Alpha-Beta Plaits / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIPHOSPHATE / ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerrer-Orta, C. / Verdaguer, N. / de la Higuera, I. / Domingo, E.
Funding support Spain, 2items
OrganizationGrant numberCountry
MINECOBIO2011-24333 Spain
MINECOBIO2011-24351 Spain
CitationJournal: J.Virol. / Year: 2015
Title: Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.
Authors: Ferrer-Orta, C. / de la Higuera, I. / Caridi, F. / Sanchez-Aparicio, M.T. / Moreno, E. / Perales, C. / Singh, K. / Sarafianos, S.G. / Sobrino, F. / Domingo, E. / Verdaguer, N.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase 3D-POL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7967
Polymers54,1101
Non-polymers6856
Water5,062281
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-7 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.700, 91.700, 118.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RNA-directed RNA polymerase 3D-POL


Mass: 54110.273 Da / Num. of mol.: 1 / Fragment: UNP RESDIUES 1830-2299 / Mutation: K20E
Source method: isolated from a genetically manipulated source
Details: This polymerase contain the mutation K20E / Source: (gene. exp.) Foot-and-mouth disease virus / Strain: isolate -/Spain/S8c1SantaPau/1970 serotype C / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03311, RNA-directed RNA polymerase
#2: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG4000, 0.2M Mg(CH3COO)2, 0.1M MES pH6.0, 4% gamma-butyrolactone
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→46.6 Å / Num. obs: 47356 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.15
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U09

1u09


Resolution: 1.8→46.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.82 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22663 2368 5 %RANDOM
Rwork0.20296 ---
obs0.20411 44977 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 41 281 4105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193908
X-RAY DIFFRACTIONr_bond_other_d0.0010.023650
X-RAY DIFFRACTIONr_angle_refined_deg0.7931.9525303
X-RAY DIFFRACTIONr_angle_other_deg0.65738382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3645488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03723.425181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63215625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1551525
X-RAY DIFFRACTIONr_chiral_restr0.0490.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4952.5641931
X-RAY DIFFRACTIONr_mcbond_other0.4952.5631930
X-RAY DIFFRACTIONr_mcangle_it0.913.8462417
X-RAY DIFFRACTIONr_mcangle_other0.913.8472418
X-RAY DIFFRACTIONr_scbond_it0.4022.651977
X-RAY DIFFRACTIONr_scbond_other0.4022.651976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.723.9512884
X-RAY DIFFRACTIONr_long_range_B_refined2.81220.5964562
X-RAY DIFFRACTIONr_long_range_B_other2.81220.5964562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 168 -
Rwork0.26 3179 -
obs--97.41 %

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