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- PDB-4nlx: Poliovirus Polymerase - G289A/C290V Loop Mutant -

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Basic information

Entry
Database: PDB / ID: 4nlx
TitlePoliovirus Polymerase - G289A/C290V 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 / ribonucleoside triphosphate phosphatase 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 ...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 / ribonucleoside triphosphate phosphatase 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 / 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 / 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 / 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: 2.6 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,6949
Polymers52,8941
Non-polymers8008
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.177, 129.177, 111.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Detailsbiological unit is the same as asym.

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Components

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


Mass: 52893.891 Da / Num. of mol.: 1 / Mutation: G289A, C290V, L446D, 455D
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.: 5 / 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.: 132 / 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

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 79.7 %
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: Mar 8, 2006
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: 2.6→29.89 Å / Num. obs: 61925 / % possible obs: 99.2 % / Redundancy: 7.55 % / Rmerge(I) obs: 0.093 / Χ2: 0.94 / Net I/σ(I): 14 / Scaling rejects: 2215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.697.450.3115.52406932300.9799.8
2.69-2.87.470.2835.8242983251199.7
2.8-2.937.480.2416.62413432201.0199.9
2.93-3.087.510.2047.52422832201.0199.8
3.08-3.287.550.1658.72466132571.02100
3.28-3.537.590.11112.82460632260.9999.4
3.53-3.887.620.07916.42488832400.9299.2
3.88-4.447.650.05721.82493132120.8398.5
4.44-5.597.670.05224.52510632240.8398.7
5.59-29.897.520.03930.12518232130.8697

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata reduction
CNSrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.858 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 3111 9.4 %Random
Rwork0.2077 ---
obs-29116 96.7 %-
Solvent computationBsol: 26.2938 Å2
Displacement parametersBiso max: 169.72 Å2 / Biso mean: 30.3509 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--4.056 Å2-6.354 Å20 Å2
2---4.056 Å20 Å2
3---8.113 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 53 132 3891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1991.5
X-RAY DIFFRACTIONc_scbond_it2.1022
X-RAY DIFFRACTIONc_mcangle_it2.0192
X-RAY DIFFRACTIONc_scangle_it3.2422.5
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
2.6-2.620.30231160.262910891205
2.62-2.640.33041120.288711601272
2.64-2.650.29341360.286910591195
2.65-2.670.29061030.253510971200
2.67-2.690.27251120.24711541266
2.69-2.710.31521380.250310961234
2.71-2.730.3359990.282111161215
2.73-2.760.26411620.244811191281
2.76-2.780.25421340.254710721206
2.78-2.80.28771050.252811651270
2.8-2.820.2584950.251610781173
2.82-2.850.26131240.253911501274
2.85-2.870.33971030.249611541257
2.87-2.90.31051230.260410901213
2.9-2.930.30761070.254811221229
2.93-2.960.23961150.23911171232
2.96-2.990.29971240.267211041228
2.99-3.020.32411170.263111001217
3.02-3.050.2595990.239811751274
3.05-3.080.27871310.264310601191
3.08-3.120.32271360.257311331269
3.12-3.150.32281010.257111591260
3.15-3.190.31281040.237811341238
3.19-3.230.2521950.240611521247
3.23-3.280.23271280.229310881216
3.28-3.320.22251130.22611341247
3.32-3.370.26221220.226211031225
3.37-3.420.23311380.22611801318
3.42-3.470.25571180.232210901208
3.47-3.530.27351400.222810821222
3.53-3.590.22821290.205211381267
3.59-3.650.20821240.215611161240
3.65-3.720.24881000.221711591259
3.72-3.80.23981320.19811431275
3.8-3.880.20321230.194610941217
3.88-3.970.27441240.185811121236
3.97-4.070.24461060.179611391245
4.07-4.180.17681330.157310971230
4.18-4.30.14631310.138411411272
4.3-4.440.18241390.142410931232
4.44-4.60.20321190.155411331252
4.6-4.780.22121360.153711301266
4.78-50.1511290.151910921221
5-5.260.2191230.168911301253
5.26-5.590.23081250.180711241249
5.59-6.020.20791240.180711211245
6.02-6.620.25351170.189711461263
6.62-7.560.19131390.174110981237
7.56-9.480.14691310.148611071238
9.48-300.16651010.18910451146
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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