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- PDB-4y3c: I304V 3D polymerase mutant of EMCV -

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Basic information

Entry
Database: PDB / ID: 4y3c
TitleI304V 3D polymerase mutant of EMCV
Components3D polymerase
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 / symbiont-mediated suppression of host gene expression / channel activity / monoatomic ion transmembrane transport / 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 / symbiont-mediated suppression of host gene expression / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / 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 / 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 / Picornavirus coat protein ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / 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 / Picornavirus coat protein / Reverse transcriptase/Diguanylate cyclase domain / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMengo encephalomyocarditis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jan 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: 3D polymerase
B: 3D polymerase
C: 3D polymerase
D: 3D polymerase
E: 3D polymerase
F: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,33917
Polymers313,3836
Non-polymers95611
Water1,27971
1
A: 3D polymerase


Theoretical massNumber of molelcules
Total (without water)52,2301
Polymers52,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3D polymerase


Theoretical massNumber of molelcules
Total (without water)52,2301
Polymers52,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3D polymerase


Theoretical massNumber of molelcules
Total (without water)52,2301
Polymers52,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6346
Polymers52,2301
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5074
Polymers52,2301
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5074
Polymers52,2301
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.332, 140.775, 171.838
Angle α, β, γ (deg.)90.00, 126.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
3D polymerase


Mass: 52230.477 Da / Num. of mol.: 6 / Mutation: I304V
Source method: isolated from a genetically manipulated source
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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.51 Å3/Da / Density % sol: 64.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 4.0M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→49.45 Å / Num. obs: 73423 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 5.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZ0

4nz0


Resolution: 3.2→138.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 64.307 / SU ML: 0.466 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24983 3697 5 %RANDOM
Rwork0.22001 ---
obs0.22154 69711 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.599 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å20 Å2-1.56 Å2
2---5.03 Å2-0 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 3.2→138.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22080 0 61 71 22212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01922672
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221594
X-RAY DIFFRACTIONr_angle_refined_deg0.7731.97130721
X-RAY DIFFRACTIONr_angle_other_deg0.673349691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.46352756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8123.2081063
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.172153849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.73115187
X-RAY DIFFRACTIONr_chiral_restr0.0460.23383
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02125428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025291
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_it0.6376.12811036
X-RAY DIFFRACTIONr_mcbond_other0.6376.12811035
X-RAY DIFFRACTIONr_mcangle_it1.1979.19113785
X-RAY DIFFRACTIONr_mcangle_other1.1979.19113786
X-RAY DIFFRACTIONr_scbond_it0.3226.14511636
X-RAY DIFFRACTIONr_scbond_other0.3226.14511636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6789.19916936
X-RAY DIFFRACTIONr_long_range_B_refined2.31448.22525004
X-RAY DIFFRACTIONr_long_range_B_other2.31448.22525004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 259 -
Rwork0.367 5119 -
obs--99.54 %
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)
10.51310.2457-0.10580.78790.14911.1793-0.0229-0.08830.04330.01990.01340.02390.07110.12460.00950.48360.0424-0.10650.55310.01160.028461.65711.929642.3274
20.81020.0866-0.14560.75070.06430.581-0.13730.02140.02890.25580.1428-0.1762-0.1053-0.0353-0.00540.66220.0186-0.14080.3913-0.10520.115754.766149.789734.7634
30.5992-0.09760.23020.8080.02520.91890.1240.0434-0.0325-0.3266-0.2265-0.0030.0056-0.09370.10250.73720.1545-0.16690.4393-0.01050.0621-0.112275.367426.7624
41.09220.0692-0.11150.50160.27771.053-0.09720.1358-0.0605-0.08670.06140.17340.13850.11470.03570.54620.0068-0.22130.4446-0.00950.14153.414-16.777337.6897
50.50540.09840.29770.6317-0.17730.65320.0785-0.10180.0017-0.11990.0370.09190.1721-0.019-0.11550.6313-0.0617-0.19230.46080.03440.076842.331223.8754-12.5125
60.41020.29790.16750.88780.230.55980.0109-0.04710.0274-0.0893-0.0184-0.0199-0.0478-0.00380.00750.60260.0531-0.18250.4174-0.01480.13031.812524.984255.3399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 460
2X-RAY DIFFRACTION2B1 - 460
3X-RAY DIFFRACTION3C1 - 460
4X-RAY DIFFRACTION4D1 - 460
5X-RAY DIFFRACTION5E1 - 460
6X-RAY DIFFRACTION6F1 - 460

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