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- PDB-2im0: Crystal structure of poliovirus polymerase complexed with CTP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 2im0
TitleCrystal structure of poliovirus polymerase complexed with CTP and Mg2+
Componentspoliovirus polymerase
KeywordsTRANSFERASE / nucleotidyltransferase / poliovirus / 3d / rna-dependent / polymerase / CTP / stabilization
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 / CYTIDINE-5'-TRIPHOSPHATE / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsThompson, A.A. / Peersen, O.B.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Stabilization of Poliovirus Polymerase by NTP Binding and Fingers-Thumb Interactions.
Authors: Thompson, A.A. / Albertini, R.A. / Peersen, O.B.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_conn.ptnr2_label_seq_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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: poliovirus polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,91410
Polymers52,9881
Non-polymers9279
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.695, 127.695, 113.034
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 poliovirus polymerase


Mass: 52987.859 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase, residues 1748-2208 / Mutation: L446D, R455D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / Gene: 3D / Plasmid: pKKT7E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLYSS / References: UniProt: P03300, RNA-directed RNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, cacodylate, dtt, pH 7.0, 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: 0.98 Å
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 49540 / Num. obs: 49540 / % possible obs: 99.7 % / Redundancy: 7.53 % / Biso Wilson estimate: 25.1 Å2 / Rsym value: 0.085 / Net I/σ(I): 3.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.82 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4957 / Rsym value: 0.462 / % possible all: 99.5

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RA6

1ra6


Resolution: 2.25→25.8 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED WITH ANOMALOUS DATA TO ACCOUNT FOR SIGNIFICANT ANOMALOUS SIGNAL FROM ARSENIC, WHICH IS FOUND IN SEVERAL CAS RESIDUES IN THE STRUCTURE. HOWEVER, THE DATA REDUCTION ...Details: THE STRUCTURE WAS REFINED WITH ANOMALOUS DATA TO ACCOUNT FOR SIGNIFICANT ANOMALOUS SIGNAL FROM ARSENIC, WHICH IS FOUND IN SEVERAL CAS RESIDUES IN THE STRUCTURE. HOWEVER, THE DATA REDUCTION AND COMPLETENESS STATISTICS ARE BASED ON MERGING ANOMALOUS REFLECTIONS. RESIDUES 132-135 HAVE POOR SIDECHAIN DENSITY AND THE MODEL REFLECTS THE BACKBONE PATH IN THIS REGION OF THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.26 9297 -RANDOM
Rwork0.237 ---
all-94567 --
obs-94567 96.7 %-
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.25 Å26.73 Å20 Å2
2--7.25 Å20 Å2
3----14.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.25→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 58 192 3957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_deg1.42

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