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- PDB-5w9g: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5w9g
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 9k (SRI-30023)
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Virus / Nuclease / Transcription / Cap-snatching / 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-KU2 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKumar, G. / White, S.
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 23, 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9196
Polymers23,1481
Non-polymers7705
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein purifies as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-31 kcal/mol
Surface area9030 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,67524
Polymers92,5934
Non-polymers3,08220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_395-x-2,-y+4,z1
crystal symmetry operation3_685-y+1,x+3,z1
crystal symmetry operation4_265y-3,-x+1,z1
Buried area6420 Å2
ΔGint-157 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.249, 90.249, 135.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C3W5S0

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-KU2 / 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4 -carboxamide / SRI-30023


Mass: 529.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25ClN4O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.8, 1.0 M AmSO4, 10 mM MnCl2, 10 mM MgCl2, 1% PVP K15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16670 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 52.05 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 1.125 / Net I/σ(I): 12.3 / Num. measured all: 125546
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.186.71.0110.7590.4061.0920.88195.6
2.18-2.267.50.8110.8540.3140.870.86699.5
2.26-2.377.80.6360.9150.2410.6810.89999.8
2.37-2.497.80.3910.9640.1490.4190.92699.9
2.49-2.657.80.2530.9830.0970.2710.94199.9
2.65-2.857.70.1670.9910.0640.1780.96199.9
2.85-3.147.70.0860.9970.0330.0921.068100
3.14-3.597.70.0590.9980.0230.0631.412100
3.59-4.527.50.0520.9980.020.0561.847100
4.52-507.10.0330.9970.0140.0361.39499.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.677 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5
RfactorNum. reflection% reflection
Rfree0.2409 862 5.17 %
Rwork0.2249 --
obs0.2258 16659 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.46 Å2 / Biso mean: 85.256 Å2 / Biso min: 47.56 Å2
Refinement stepCycle: final / Resolution: 2.1→38.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 44 17 1450
Biso mean--105.27 75.48 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031461
X-RAY DIFFRACTIONf_angle_d0.6071976
X-RAY DIFFRACTIONf_chiral_restr0.041212
X-RAY DIFFRACTIONf_plane_restr0.003254
X-RAY DIFFRACTIONf_dihedral_angle_d4.224911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0972-2.22860.38611140.29652530264496
2.2286-2.40070.32131350.275626012736100
2.4007-2.64220.26121530.260626102763100
2.6422-3.02440.35751560.265726112767100
3.0244-3.80990.28521360.236526632799100
3.8099-38.68310.19111680.197527822950100
Refinement TLS params.Method: refined / Origin x: -66.154 Å / Origin y: 173.298 Å / Origin z: 288.573 Å
111213212223313233
T0.5435 Å20.1475 Å2-0.1184 Å2-0.9203 Å20.4239 Å2--0.6781 Å2
L2.6167 °20.8273 °2-0.0255 °2-4.2018 °20.3074 °2--3.1998 °2
S-0.4427 Å °-0.6333 Å °-0.2575 Å °0.4238 Å °0.0028 Å °-0.5071 Å °0.0651 Å °0.965 Å °0.2957 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 204:204 ) )A-2 - 176
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 204:204 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 204:204 ) )A202
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 204:204 ) )A204

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