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- PDB-4nlu: Poliovirus Polymerase - G289A Loop Mutant -

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Basic information

Entry
Database: PDB / ID: 4nlu
TitlePoliovirus Polymerase - G289A Loop Mutant
ComponentsRNA-directed RNA polymerase 3D-POL
KeywordsViral Protein / hydrolase / polymerase / RNA dependent RNA polymerase / RdRP / virus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity ...symbiont-mediated suppression of host translation initiation / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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) / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
ACETIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSholders, A.J. / Peersen, O.B.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Distinct conformations of a putative translocation element in poliovirus polymerase.
Authors: Sholders, A.J. / Peersen, O.B.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase 3D-POL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,86210
Polymers53,0021
Non-polymers8609
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.093, 129.093, 112.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein RNA-directed RNA polymerase 3D-POL / P3D-POL / Genome polyprotein


Mass: 53001.887 Da / Num. of mol.: 1 / Mutation: G289A, L446D, R455D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P03300, RNA-directed RNA polymerase
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Grown in sodium acetate, cacodylate, DTT. Transferred to 250 mM sodium acetate, 30% (w/v) PEG-400, 0.1 M cacodylic acid, and 2 mM DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 6, 2005
RadiationMonochromator: double flat Si crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→42.26 Å / Num. obs: 77401 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.061 / Χ2: 0.97 / Net I/σ(I): 11 / Scaling rejects: 3978
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2
1.95-2.026.680.49725221477221.48
2.02-2.16.720.3872.75218076931.32
2.1-2.26.740.2963.65262577431.22
2.2-2.316.710.2244.85242676961.17
2.31-2.466.790.1616.45283177201
2.46-2.656.830.1198.55318777310.9
2.65-2.916.860.08610.95341777310.78
2.91-3.336.90.06114.65362877480.67
3.33-4.26.910.04421.75383277660.61
4.2-42.266.850.02833.55392978510.57

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Processing

Software
NameVersionClassificationNB
d*TREK9.4LDzdata reduction
CNSrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RA6

1ra6


Resolution: 2.1→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8156 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 11446 9.4 %Random
Rwork0.2251 ---
obs-67705 94.7 %-
Solvent computationBsol: 43.7474 Å2
Displacement parametersBiso max: 152.22 Å2 / Biso mean: 37.1549 Å2 / Biso min: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1--4.989 Å2-5.155 Å20 Å2
2---4.989 Å20 Å2
3---9.978 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 57 244 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2511.5
X-RAY DIFFRACTIONc_scbond_it2.3442
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scangle_it3.3732.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.110.30982020.307520602262
2.11-2.130.32812060.324419332139
2.13-2.140.32912160.294720122228
2.14-2.160.26422260.285819182144
2.16-2.180.32492530.311619812234
2.18-2.190.2992210.308519322153
2.19-2.210.35232010.280819832184
2.21-2.230.29042010.283420652266
2.23-2.240.26821800.272619812161
2.24-2.260.31672330.268321442377
2.26-2.280.34392220.278619872209
2.28-2.30.27252120.270520312243
2.3-2.320.26922220.266620422264
2.32-2.340.29361960.270220812277
2.34-2.370.25912280.263120182246
2.37-2.390.29242470.253220252272
2.39-2.410.26672210.251320462267
2.41-2.440.32112320.259320632295
2.44-2.460.27922140.242620562270
2.46-2.490.30342330.265220802313
2.49-2.520.27192510.253421162367
2.52-2.550.28322300.263520172247
2.55-2.580.26442310.236521202351
2.58-2.610.34432160.243820962312
2.61-2.650.28182590.259420922351
2.65-2.680.26062060.239521682374
2.68-2.720.27912580.249620632321
2.72-2.760.26242560.253720992355
2.76-2.80.23572180.24521432361
2.8-2.850.2892070.260121022309
2.85-2.90.29162220.239521302352
2.9-2.950.27522300.248621332363
2.95-3.010.28092170.25621372354
3.01-3.070.29052020.259421272329
3.07-3.140.30092420.27321422384
3.14-3.210.26682140.250321292343
3.21-3.290.29462500.247221612411
3.29-3.380.25842620.238820992361
3.38-3.480.25112160.230821622378
3.48-3.590.2152220.218821672389
3.59-3.720.23322610.211421442405
3.72-3.870.20852150.201321562371
3.87-4.040.21132440.187121602404
4.04-4.250.19892540.164721232377
4.25-4.520.17862380.155721662404
4.52-4.870.1572300.159421602390
4.87-5.350.19622440.190321682412
5.35-6.120.21342630.205921692432
6.12-7.690.2242640.210121432407
7.69-300.21792580.187121842442
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep3.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ajs2.param
X-RAY DIFFRACTION5ntps.param

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