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- PDB-4y2c: M300V 3D polymerase mutant of EMCV -

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Basic information

Entry
Database: PDB / ID: 4y2c
TitleM300V 3D polymerase mutant of EMCV
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / RNA dependent RNA polymerase Cardiovirus Inhibitor resistance
Function / homology
Function and homology information


positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / 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 / 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. / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMengo encephalomyocarditis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C. / Vives-Adrian, L.
CitationJournal: Plos Pathog. / Year: 2015
Title: The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family.
Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, ...Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, P. / Lacroix, C. / Purstinger, G. / Coutard, B. / Canard, B. / Boehr, D.D. / Arnold, J.J. / Cameron, C.E. / Verdaguer, N. / Neyts, J. / van Kuppeveld, F.J.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5815
Polymers52,2121
Non-polymers3684
Water3,171176
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-5 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.632, 122.632, 198.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-639-

HOH

31A-665-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 52212.438 Da / Num. of mol.: 1 / Fragment: residues 1834-2293 / Mutation: M300V
Source method: isolated from a genetically manipulated source
Details: M300V 3Dpolymerase mutant / Source: (gene. exp.) Mengo encephalomyocarditis virus / Plasmid: pEGT20A / Production host: Escherichia coli (E. coli)
References: UniProt: P12296, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.45 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10%PEG6000 2.0M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→43.36 Å / Num. obs: 36208 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYZ

4nyz


Resolution: 2.2→43.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.019 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24906 1805 5 %RANDOM
Rwork0.21564 ---
obs0.21731 34387 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å20 Å2
2--0.31 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.2→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 24 176 3875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193815
X-RAY DIFFRACTIONr_bond_other_d0.0010.023639
X-RAY DIFFRACTIONr_angle_refined_deg0.871.9725171
X-RAY DIFFRACTIONr_angle_other_deg0.69238376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6875467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49723.184179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1641532
X-RAY DIFFRACTIONr_chiral_restr0.0520.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
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_it0.5852.6791853
X-RAY DIFFRACTIONr_mcbond_other0.5852.6791852
X-RAY DIFFRACTIONr_mcangle_it1.0754.0182319
X-RAY DIFFRACTIONr_mcangle_other1.0754.0182320
X-RAY DIFFRACTIONr_scbond_it0.4822.6941962
X-RAY DIFFRACTIONr_scbond_other0.4822.6941962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8774.0182851
X-RAY DIFFRACTIONr_long_range_B_refined2.67420.8554310
X-RAY DIFFRACTIONr_long_range_B_other2.67420.8554310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 142 -
Rwork0.309 2574 -
obs--97.45 %
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)
10.5882-0.31140.52691.5740.07852.3006-0.0420.06060.1458-0.23270.0048-0.1419-0.14880.36490.03710.098-0.00450.01390.10150.00540.0449-7.6107-29.2783-23.9134
20.5186-0.20060.37220.94650.27191.23230.0221-0.01590.0415-0.1553-0.030.083-0.03980.08390.00790.14660.0184-0.00220.1032-0.00210.0242-13.4308-31.2566-23.7719
37.2797-2.0909-0.17470.60520.06040.0281-0.1477-0.289-0.38570.02890.12880.1126-0.0080.11030.01890.3993-0.09280.03390.46580.060.0875-11.9037-29.1247-25.8746
400000000000000-00.099000.09900.099000
500000000000000-00.099000.09900.099000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 460
2X-RAY DIFFRACTION2C2 - 240
3X-RAY DIFFRACTION3B507 - 512

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