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- PDB-2ijf: Crystal Structure of the Poliovirus RNA-Dependent RNA Polymerase ... -

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Basic information

Entry
Database: PDB / ID: 2ijf
TitleCrystal Structure of the Poliovirus RNA-Dependent RNA Polymerase Fidelity Mutant 3Dpol G64S
ComponentsRNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerase / fidelity / RNA polymerase / poliovirus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity ...symbiont-mediated suppression of host translation initiation / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / nucleus
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 / 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 ...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 / 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) / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMarcotte, L.L. / Gohara, D.G. / Filman, D.J. / Hogle, J.M.
CitationJournal: J.Virol. / Year: 2007
Title: Crystal structure of poliovirus 3CD: virally-encoded protease and precursor to the RNA-dependent RNA polymerase.
Authors: Marcotte, L.L. / Wass, A.B. / Gohara, D.W. / Pathak, H.B. / Arnold, J.J. / Filman, D.J. / Cameron, C.E. / Hogle, J.M.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)52,6021
Polymers52,6021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.843, 125.843, 113.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase


Mass: 52601.953 Da / Num. of mol.: 1 / Mutation: G64S, L446D, R455D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / Gene: 3D / Production host: Escherichia coli (E. coli)
References: UniProt: P03300, UniProt: Q8QXN9*PLUS, RNA-directed RNA polymerase

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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: 4.92 Å3/Da / Density % sol: 74.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M sodium acetate, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 20317 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 %
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.7 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1RA6

1ra6


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 34.668 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.592 / ESU R Free: 0.328
RfactorNum. reflection% reflectionSelection details
Rfree0.24447 1038 5.1 %RANDOM
Rwork0.21165 ---
obs0.21322 19216 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 89.24 Å2
Baniso -1Baniso -2Baniso -3
1-6.84 Å23.42 Å20 Å2
2--6.84 Å20 Å2
3----10.26 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 0 0 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223787
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9665124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.4355460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.80324.294170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.88815674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.991517
X-RAY DIFFRACTIONr_chiral_restr0.1120.2556
X-RAY DIFFRACTIONr_gen_planes_refined00.022848
X-RAY DIFFRACTIONr_nbd_refined0.2330.21616
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.222
X-RAY DIFFRACTIONr_mcbond_it2.02622344
X-RAY DIFFRACTIONr_mcangle_it3.32843716
X-RAY DIFFRACTIONr_scbond_it4.40741638
X-RAY DIFFRACTIONr_scangle_it6.42261408
LS refinement shellResolution: 3.002→3.16 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 146 -
Rwork0.393 2683 -
obs--97.79 %
Refinement TLS params.Method: refined / Origin x: 59.1593 Å / Origin y: 2.8303 Å / Origin z: 6.129 Å
111213212223313233
T-0.4566 Å20.0611 Å2-0.0025 Å2--0.5599 Å20.0057 Å2---0.3917 Å2
L1.2179 °2-0.1232 °20.8859 °2-2.0615 °2-0.7153 °2--5.3774 °2
S-0.0699 Å °-0.3075 Å °0.1189 Å °0.2144 Å °0.0543 Å °-0.222 Å °-0.5687 Å °-0.8536 Å °0.0156 Å °

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