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- PDB-4k4t: Poliovirus polymerase elongation complex (r4_form) -

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Basic information

Entry
Database: PDB / ID: 4k4t
TitlePoliovirus polymerase elongation complex (r4_form)
Components
  • RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')
  • RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
  • RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')
  • RNA-directed RNA polymerase 3D-POL
Keywordstransferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / transferase-rna complex
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
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGong, P. / Peersen, O.B.
CitationJournal: Plos One / Year: 2013
Title: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
Authors: Gong, P. / Kortus, M.G. / Nix, J.C. / Davis, R.E. / Peersen, O.B.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
E: RNA-directed RNA polymerase 3D-POL
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')
G: RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,71214
Polymers135,2138
Non-polymers4996
Water1,76598
1
A: RNA-directed RNA polymerase 3D-POL
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8567
Polymers67,6074
Non-polymers2503
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-67 kcal/mol
Surface area23960 Å2
MethodPISA
2
E: RNA-directed RNA polymerase 3D-POL
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')
G: RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8567
Polymers67,6074
Non-polymers2503
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-65 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.401, 59.248, 97.455
Angle α, β, γ (deg.)78.110, 78.090, 78.850
Int Tables number1
Space group name H-MP1
Detailschains (A,B,C,D) and chains (E,F,G,H)

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Components

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Protein , 1 types, 2 molecules AE

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


Mass: 53761.195 Da / Num. of mol.: 2 / Fragment: unp residues 1749-2209 / Mutation: L446D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Production host: Escherichia coli (E. coli) / References: UniProt: P03300, RNA-directed RNA polymerase

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RNA chain , 3 types, 6 molecules BFCGDH

#2: RNA chain RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*GP*AP*AP*A)-3')


Mass: 7018.227 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3')


Mass: 3852.344 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: RNA chain RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')


Mass: 2974.854 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 104 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.16 M MgCl2, 0.08 M Tris-HCl, 24% (w/v) PEG 4000, 20% (v/v) glycerol and directly frozen for data collection , VAPOR DIFFUSION, SITTING 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→46.96 Å / Num. obs: 31399 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 1.91 % / Rmerge(I) obs: 0.069 / Χ2: 1.03 / Net I/σ(I): 6.8 / Scaling rejects: 454
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.75-2.851.910.4681.8605031491.1795.6
2.85-2.961.920.3692.2606231561.195.9
2.96-3.11.920.312.6603731311.0896.2
3.1-3.261.920.2363.4602731261.0496
3.26-3.461.90.1854.260293140196.4
3.46-3.731.910.1385.7604531470.9996.4
3.73-4.111.910.1117.6602331351.0196.3
4.11-4.71.910.08310.3606631500.9896.2
4.7-5.921.910.05414.9608531310.9295.8
5.92-46.961.920.06414.9608431341.0296.1

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.1Ldata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→46.959 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7707 / SU ML: 0.4 / σ(F): 1.96 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1602 5.11 %Random
Rwork0.2016 ---
obs0.2047 31380 96.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.43 Å2 / Biso mean: 67.9464 Å2 / Biso min: 36.22 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 1418 26 98 8944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099184
X-RAY DIFFRACTIONf_angle_d1.21612728
X-RAY DIFFRACTIONf_chiral_restr0.0521440
X-RAY DIFFRACTIONf_plane_restr0.0071370
X-RAY DIFFRACTIONf_dihedral_angle_d17.63606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.83880.31371320.30262735286795
2.8388-2.94020.35451690.2882671284096
2.9402-3.05790.33581420.28062684282696
3.0579-3.19710.35411420.26252717285996
3.1971-3.36560.35341620.27212697285996
3.3656-3.57640.27231390.22842727286697
3.5764-3.85240.31211520.2042694284696
3.8524-4.23980.23111420.17532745288796
4.2398-4.85280.21071290.15882712284196
4.8528-6.11190.22811470.18322699284696
6.1119-46.96560.22941460.17922697284396

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