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- PDB-4wzq: Mutant K20E of RNA dependent RNA polymerase 3D from Foot-and-Mout... -

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Basic information

Entry
Database: PDB / ID: 4wzq
TitleMutant K20E of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with RNA
Components
  • RNA dependent-RNA polymerase 3D
  • RNA template
  • RNAprimer
KeywordsTRANSFERASE / RNA dependent RNA polymerase / Nuclear Localization Signal / Picornavirus / closed right-hand
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 / nucleoside-triphosphate phosphatase / regulation of translation / 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 / nucleoside-triphosphate phosphatase / regulation of translation / 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 / 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
: / RNA / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C.
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 3D
B: RNA template
C: RNAprimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9864
Polymers58,9313
Non-polymers551
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-46 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.160, 95.160, 101.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA dependent-RNA polymerase 3D


Mass: 54177.340 Da / Num. of mol.: 1 / Fragment: UNP residues 1858-2328 / Mutation: K20E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Gene: CDS / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A4H1Z0, UniProt: P03311*PLUS
#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 RNAprimer


Mass: 2212.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30%PEG 4000, 0.2M Mg(CH3COO)2, 0.1M MES pH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.5 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: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.8→43.16 Å / Num. obs: 13460 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACrigid body refinement using PDB id 1wne as a modelphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wne

1wne


Resolution: 2.8→43.16 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.885 / SU B: 41.101 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27087 726 5.4 %RANDOM
Rwork0.24943 ---
obs0.25052 12712 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.586 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 314 1 12 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194197
X-RAY DIFFRACTIONr_bond_other_d0.0010.023751
X-RAY DIFFRACTIONr_angle_refined_deg0.6881.8825758
X-RAY DIFFRACTIONr_angle_other_deg0.67438634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4295477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76923.405185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41315631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.7771528
X-RAY DIFFRACTIONr_chiral_restr0.0430.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021002
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_it0.2353.6091905
X-RAY DIFFRACTIONr_mcbond_other0.2353.6081904
X-RAY DIFFRACTIONr_mcangle_it0.4315.4132380
X-RAY DIFFRACTIONr_mcangle_other0.4315.4142381
X-RAY DIFFRACTIONr_scbond_it0.1513.6352291
X-RAY DIFFRACTIONr_scbond_other0.1513.6352290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2785.4513377
X-RAY DIFFRACTIONr_long_range_B_refined1.07229.4534754
X-RAY DIFFRACTIONr_long_range_B_other1.07229.4554755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 54 -
Rwork0.343 900 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0754-0.85570.52186.3609-0.38271.96990.07640.1568-0.04610.126-0.13960.56920.1612-0.37460.06330.05050.03760.00360.2969-0.0880.081419.176726.304924.7199
213.149710.65777.230111.34423.54156.432-0.26370.05730.5848-0.35470.19581.2528-0.0622-0.29710.06790.49030.12670.07580.5832-0.16140.664213.556933.820130.1418
38.9827-7.18880.634113.37825.11724.2243-0.2348-0.3634-0.11880.8877-0.19330.65790.4751-0.52860.42820.37490.0638-0.04310.689-0.09640.574112.35438.488527.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 476
2X-RAY DIFFRACTION2B903 - 910
3X-RAY DIFFRACTION3C914 - 920

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