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- PDB-5w3i: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5w3i
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 6e (SRI-29685)
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / nuclease / transcription / cap-snatching / virus / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GY5 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI098757 United States
St. Jude Children's Research Hospital (ALSAC) United States
St. Jude Children's Research Hospital (ALSAC) United States
CitationJournal: Sci Rep / Year: 2017
Title: Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease.
Authors: Beylkin, D. / Kumar, G. / Zhou, W. / Park, J. / Jeevan, T. / Lagisetti, C. / Harfoot, R. / Webby, R.J. / White, S.W. / Webb, T.R.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2725
Polymers23,6541
Non-polymers6184
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein purifies as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-8 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.162, 61.162, 94.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Polymerase acidic protein


Mass: 23653.916 Da / Num. of mol.: 1 / Mutation: Residues 51-72 replaced with a GGS linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W5S0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GY5 / 5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxamide / SRI-29685


Mass: 416.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M Succinic Acid pH 7.0, 5 mM MnCl2, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 15487 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 18.07 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Χ2: 0.937 / Net I/σ(I): 12.5 / Num. measured all: 173689
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0210.30.9550.8880.3011.0030.809100
2.02-2.111.10.6810.9350.2090.7130.886100
2.1-2.211.30.450.9760.1370.4710.913100
2.2-2.3111.30.3080.9780.0940.3230.971100
2.31-2.4611.40.2180.9860.0660.2280.983100
2.46-2.6511.40.1420.9930.0430.1491.013100
2.65-2.9111.60.1020.9950.0310.1071.033100
2.91-3.3311.60.0750.9960.0230.0791.127100
3.33-4.211.50.0540.9970.0160.0561.062100
4.2-4010.70.0330.9980.0110.0350.55599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.325 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7
RfactorNum. reflection% reflection
Rfree0.2011 740 4.88 %
Rwork0.1753 --
obs0.1766 15151 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.03 Å2 / Biso mean: 27.6948 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.95→35.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 70 80 1573
Biso mean--39.44 32.78 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061488
X-RAY DIFFRACTIONf_angle_d0.7552005
X-RAY DIFFRACTIONf_chiral_restr0.046217
X-RAY DIFFRACTIONf_plane_restr0.004255
X-RAY DIFFRACTIONf_dihedral_angle_d20.425881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9497-2.10020.2253990.20112593269289
2.1002-2.31150.2131670.174128883055100
2.3115-2.64590.22141550.169229253080100
2.6459-3.33320.21971460.179729373083100
3.3332-35.33040.1791730.169530683241100
Refinement TLS params.Method: refined / Origin x: 22.5823 Å / Origin y: -17.0868 Å / Origin z: 0.67 Å
111213212223313233
T0.1472 Å2-0.0819 Å20.007 Å2-0.1236 Å2-0.0233 Å2--0.0872 Å2
L1.1515 °20.2917 °20.4096 °2-2.0026 °20.4448 °2--0.8389 °2
S-0.0021 Å °-0.0356 Å °-0.0447 Å °0.0465 Å °0.0366 Å °-0.0622 Å °0.0171 Å °0.0288 Å °-0.0269 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 201
2X-RAY DIFFRACTION1allB201 - 202
3X-RAY DIFFRACTION1allW1 - 181
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allC1

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