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- PDB-4zpb: Coxsackievirus B3 Polymerase - F364W mutant -

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Basic information

Entry
Database: PDB / ID: 4zpb
TitleCoxsackievirus B3 Polymerase - F364W mutant
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / : / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.797 Å
AuthorsPeersen, O.B. / McDonald, S.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Design of a Genetically Stable High Fidelity Coxsackievirus B3 Polymerase That Attenuates Virus Growth in Vivo.
Authors: McDonald, S. / Block, A. / Beaucourt, S. / Moratorio, G. / Vignuzzi, M. / Peersen, O.B.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)52,5161
Polymers52,5161
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 74.610, 289.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1111-

HOH

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Components

#1: Protein RNA-directed RNA polymerase


Mass: 52516.086 Da / Num. of mol.: 1 / Fragment: unp residues 1724-2185 / Mutation: F364W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Plasmid: pET26/Ub / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5UEA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085 M Tris pH 7.5, 1.2 M Ammonium Sulfate , 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.797→52.757 Å / Num. obs: 144867 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 19.97 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.098 / Χ2: 0.993 / Net I/σ(I): 14.79 / Num. measured all: 1052868
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.910.7620.6642.3515229323530230610.72198
1.91-2.040.9090.3824.3614924122103221020.413100
2.04-2.20.970.237.814951120578205770.248100
2.2-2.410.9870.15311.8614574618911189110.165100
2.41-2.690.9930.11116.5213207517084170840.119100
2.69-3.110.9960.07823.5811632615136151360.084100
3.11-3.810.9980.05732.339434312710127100.061100
3.81-5.370.9980.05136.372143986598650.054100
5.370.9980.04836.6641190542954210.05199.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 1.797→52.757 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 3736 2.58 %
Rwork0.1878 --
obs0.1888 144867 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.797→52.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 0 654 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083787
X-RAY DIFFRACTIONf_angle_d0.8345129
X-RAY DIFFRACTIONf_dihedral_angle_d12.1882260
X-RAY DIFFRACTIONf_chiral_restr0.053558
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7973-1.820.33271320.31514885X-RAY DIFFRACTION91
1.82-1.8440.3131400.26415137X-RAY DIFFRACTION100
1.844-1.86930.26821400.25455281X-RAY DIFFRACTION100
1.8693-1.8960.30311390.24885235X-RAY DIFFRACTION100
1.896-1.92430.2661370.23775235X-RAY DIFFRACTION100
1.9243-1.95430.26371410.23085264X-RAY DIFFRACTION100
1.9543-1.98640.26821370.21565241X-RAY DIFFRACTION100
1.9864-2.02060.24861410.21395233X-RAY DIFFRACTION100
2.0206-2.05740.25241420.215206X-RAY DIFFRACTION100
2.0574-2.09690.21611370.20795228X-RAY DIFFRACTION100
2.0969-2.13980.29191380.20275311X-RAY DIFFRACTION100
2.1398-2.18630.19131420.19055248X-RAY DIFFRACTION100
2.1863-2.23710.22941370.18855188X-RAY DIFFRACTION100
2.2371-2.29310.26021420.19015260X-RAY DIFFRACTION100
2.2931-2.35510.20091380.18755241X-RAY DIFFRACTION100
2.3551-2.42440.20271450.18695253X-RAY DIFFRACTION100
2.4244-2.50260.20751380.18215256X-RAY DIFFRACTION100
2.5026-2.59210.28211310.19295239X-RAY DIFFRACTION100
2.5921-2.69590.2451400.18915224X-RAY DIFFRACTION100
2.6959-2.81850.20931400.19375234X-RAY DIFFRACTION100
2.8185-2.96710.24491380.19595257X-RAY DIFFRACTION100
2.9671-3.1530.22261420.18445234X-RAY DIFFRACTION100
3.153-3.39640.22011380.17635286X-RAY DIFFRACTION100
3.3964-3.73810.20341310.16715231X-RAY DIFFRACTION100
3.7381-4.27880.18911350.15285240X-RAY DIFFRACTION100
4.2788-5.390.17361420.15525240X-RAY DIFFRACTION100
5.39-52.780.24441330.18435244X-RAY DIFFRACTION100

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