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- PDB-4k4s: Poliovirus polymerase elongation complex (r3_form) -

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Basic information

Entry
Database: PDB / ID: 4k4s
TitlePoliovirus polymerase elongation complex (r3_form)
Components
  • RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*CP*GP*AP*AP*A)-3')
  • RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*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: 2.4 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*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*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*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)137,10515
Polymers136,5148
Non-polymers5917
Water4,288238
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*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*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)68,5998
Polymers68,2574
Non-polymers3424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*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)68,5077
Polymers68,2574
Non-polymers2503
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.768, 58.859, 97.586
Angle α, β, γ (deg.)77.880, 77.800, 79.970
Int Tables number1
Space group name H-MP1

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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*CP*GP*AP*AP*A)-3')


Mass: 7323.408 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*UP*GP*UP*UP*CP*GP*CP*GP*AP*GP*AP*GP*A)-3')


Mass: 4197.550 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, 245 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: sitting drop, temperature 289K, VAPOR DIFFUSION, SITTING DROP

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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: 2.4→39.93 Å / Num. obs: 47355 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 1.91 % / Rmerge(I) obs: 0.066 / Χ2: 1.03 / Net I/σ(I): 6.2 / Scaling rejects: 686
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.491.920.5211.5908747211.1197.5
2.49-2.591.920.4431.8920547791.0897.6
2.59-2.71.920.3512.3913047471.0997.6
2.7-2.851.920.2892.8898746741.0897.9
2.85-3.021.920.2063.7920447811.0498
3.02-3.261.920.164.8919747770.9998.3
3.26-3.581.910.1176.5907747310.9898.4
3.58-4.11.90.0919.2914147650.9698.2
4.1-5.171.90.06214.1913646870.9196.8
5.17-39.931.920.06815.3915446931.0397

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.9.1Ldata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.922 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7552 / SU ML: 0.37 / σ(F): 1.98 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 2407 5.08 %Random
Rwork0.1976 ---
obs0.2001 47337 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.79 Å2 / Biso mean: 58.2933 Å2 / Biso min: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 1431 32 238 9103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099203
X-RAY DIFFRACTIONf_angle_d1.12912756
X-RAY DIFFRACTIONf_chiral_restr0.0481443
X-RAY DIFFRACTIONf_plane_restr0.0061371
X-RAY DIFFRACTIONf_dihedral_angle_d16.0423618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4490.36931480.32362717286598
2.449-2.50220.39531320.32162591272397
2.5022-2.56040.33211570.29692665282298
2.5604-2.62440.35841380.26232597273598
2.6244-2.69540.36221280.27072685281398
2.6954-2.77470.33491260.25512643276998
2.7747-2.86420.36521380.26322640277898
2.8642-2.96660.2911630.26162628279198
2.9666-3.08530.33371380.24312694283298
3.0853-3.22560.32651480.23122607275599
3.2256-3.39560.27921550.21792621277698
3.3956-3.60820.25831380.2062698283699
3.6082-3.88660.21471450.16912652279798
3.8866-4.27730.21221350.15132652278798
4.2773-4.89530.1851320.14882634276696
4.8953-6.16390.17381410.16992607274897
6.1639-39.92760.21531450.18922599274496

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