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- PDB-4wzm: Mutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth D... -

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Basic information

Entry
Database: PDB / ID: 4wzm
TitleMutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth Disease Virus complexed with RNA
Components
  • RNA dependent RNA polymerase
  • RNA primer
  • RNA template
KeywordsTRANSFERASE / Picornavirus / Nuclear Localization Signal
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / 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 / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / 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 / viral protein processing / RNA helicase activity / 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 / host cell nucleus / virion attachment to host cell / 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 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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
ACETATE ION / : / RNA / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C. / de la Higuera, N.
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 20, 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 dependent RNA polymerase
B: RNA template
C: RNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1627
Polymers58,8643
Non-polymers2984
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-43 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.306, 94.306, 100.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA dependent RNA polymerase


Mass: 54110.273 Da / Num. of mol.: 1 / Fragment: UNP residues 1830-2327 / Mutation: K18E
Source method: isolated from a genetically manipulated source
Details: It's the mutant K18E of RdRP from FMDV / 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

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA template


Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA primer


Mass: 2212.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 39 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 4K; 0.2M Mg(CH3COO)2, 0.1M MES pH6.0; 4% gamma- butyrolactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.57→63.63 Å / Num. obs: 18038 / % possible obs: 99 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.3
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNE

1wne


Resolution: 2.52→81.67 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.508 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 1.5 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26156 848 4.7 %RANDOM
Rwork0.22449 ---
obs0.22623 17053 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.52→81.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 317 17 35 4101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194198
X-RAY DIFFRACTIONr_bond_other_d0.0010.023762
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.8865752
X-RAY DIFFRACTIONr_angle_other_deg0.73138662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0445476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15323.443183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30315631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9521528
X-RAY DIFFRACTIONr_chiral_restr0.0580.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
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_it2.2036.2081904
X-RAY DIFFRACTIONr_mcbond_other2.26.2061903
X-RAY DIFFRACTIONr_mcangle_it3.7279.3072380
X-RAY DIFFRACTIONr_mcangle_other3.7269.3092381
X-RAY DIFFRACTIONr_scbond_it1.9526.7862294
X-RAY DIFFRACTIONr_scbond_other1.9516.7862293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.34510.1623373
X-RAY DIFFRACTIONr_long_range_B_refined6.51453.0554842
X-RAY DIFFRACTIONr_long_range_B_other6.51453.0584843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 65 -
Rwork0.345 1212 -
obs--98.46 %

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