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- PDB-4x2b: K20A RNA dependent RNA polymerase mutant from Foot-and-Mouth dise... -

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Basic information

Entry
Database: PDB / ID: 4x2b
TitleK20A RNA dependent RNA polymerase mutant from Foot-and-Mouth disease Virus complexed with an RNA
Components
  • RNA dependent RNA polymerase
  • RNA primer
  • RNA template
KeywordsTRANSFERASE / Nuclear Signal Localization / Picornavirus / Foot-and-Mouth disease / Virus / RNA dependent RNA polymerase / 3D polymerase
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
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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 26, 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)58,2194
Polymers58,1953
Non-polymers241
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-39 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.222, 94.222, 121.515
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 dependent RNA polymerase


Mass: 54052.238 Da / Num. of mol.: 1 / Fragment: UNP residues 1858-2327 / Mutation: E20A
Source method: isolated from a genetically manipulated source
Details: This protein is the mutant K20A / 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: RNA chain RNA template


Mass: 2236.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA primer


Mass: 1906.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4000, 0.2M MES pH 6.0, 0.1 M Mg(COO3)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979469 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979469 Å / Relative weight: 1
ReflectionResolution: 2.94→47.11 Å / Num. obs: 12228 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.8
Reflection shellResolution: 2.94→3.09 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8

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Processing

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

1u09


Resolution: 2.94→47.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU B: 42 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25858 583 4.8 %RANDOM
Rwork0.21508 ---
obs0.21722 11606 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2--0.15 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.94→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 280 1 14 4048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194155
X-RAY DIFFRACTIONr_bond_other_d0.0010.023739
X-RAY DIFFRACTIONr_angle_refined_deg0.7631.8895690
X-RAY DIFFRACTIONr_angle_other_deg0.67338606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2085476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28823.407182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35915632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4061527
X-RAY DIFFRACTIONr_chiral_restr0.0490.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
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_it0.7864.8281907
X-RAY DIFFRACTIONr_mcbond_other0.7844.8281906
X-RAY DIFFRACTIONr_mcangle_it1.4197.2422382
X-RAY DIFFRACTIONr_mcangle_other1.4197.2432383
X-RAY DIFFRACTIONr_scbond_it0.6845.5372248
X-RAY DIFFRACTIONr_scbond_other0.6845.5352247
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1898.3323308
X-RAY DIFFRACTIONr_long_range_B_refined4.51943.9294684
X-RAY DIFFRACTIONr_long_range_B_other4.51743.9444683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.936→3.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 38 -
Rwork0.327 815 -
obs--96.17 %
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)
13.4543-1.4005-0.11650.97740.20021.0550.20.16230.0202-0.3417-0.0874-0.0844-0.12480.0638-0.11260.2337-0.08590.03490.21950.02990.02622.129725.793830.9347
200000000000000-00.2177000.217700.2177000
300000000000000-00.2177000.217700.2177000
400000000000000-00.2177000.217700.2177000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 477
2X-RAY DIFFRACTION2C1 - 103
3X-RAY DIFFRACTION3D511 - 514
4X-RAY DIFFRACTION4B1

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