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

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Basic information

Entry
Database: PDB / ID: 5wap
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 10i (SRI-30025)
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-KU9 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 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 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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
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.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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8795
Polymers23,1481
Non-polymers7314
Water18010
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 area350 Å2
ΔGint-23 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.653, 90.653, 135.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-KU9 / 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 525.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25ClN4O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M CAPSO pH 9.5, 1 M Ammonium sulfate, 10 mM MnCl2, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14620 / % possible obs: 99.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 54.98 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Rrim(I) all: 0.079 / Χ2: 1.15 / Net I/σ(I): 14.5 / Num. measured all: 122464
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.70.8130.7880.3240.8790.80697.5
2.28-2.3780.7990.8850.30.8550.824100
2.37-2.488.70.5690.9470.2040.6050.868100
2.48-2.618.80.4340.960.1550.4610.898100
2.61-2.778.80.3070.9790.110.3270.976100
2.77-2.998.80.1770.9910.0630.1891.121100
2.99-3.298.70.0990.9960.0350.1051.251100
3.29-3.768.70.0680.9970.0250.0731.415100
3.76-4.748.50.0630.9970.0230.0671.572100
4.74-5080.0520.9980.020.0551.62999.4

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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: 2.201→33.792 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.32
RfactorNum. reflection% reflection
Rfree0.2447 693 4.74 %
Rwork0.226 --
obs0.2269 14614 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.44 Å2 / Biso mean: 82.9871 Å2 / Biso min: 50.04 Å2
Refinement stepCycle: final / Resolution: 2.201→33.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 43 10 1457
Biso mean--90.66 77.53 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021479
X-RAY DIFFRACTIONf_angle_d0.4822004
X-RAY DIFFRACTIONf_chiral_restr0.038213
X-RAY DIFFRACTIONf_plane_restr0.003258
X-RAY DIFFRACTIONf_dihedral_angle_d7.1886
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 (%)
2.201-2.37090.3421400.29312676281699
2.3709-2.60940.26891640.25527112875100
2.6094-2.98680.2741270.26627832910100
2.9868-3.76220.28971240.256128162940100
3.7622-33.79650.21521380.197529353073100
Refinement TLS params.Method: refined / Origin x: -66.335 Å / Origin y: 355.214 Å / Origin z: 693.823 Å
111213212223313233
T0.621 Å20.154 Å2-0.0943 Å2-0.9544 Å20.3829 Å2--0.6314 Å2
L2.0732 °20.6119 °20.5598 °2-3.4611 °20.0975 °2--2.2241 °2
S-0.3254 Å °-0.4725 Å °-0.1331 Å °0.4099 Å °-0.0567 Å °-0.4887 Å °0.1249 Å °0.8678 Å °0.2843 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -3:195 OR RESID 301:310 OR RESID 201:202 OR RESID 204:204 OR RESID 203:203 ) )A-3 - 195
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -3:195 OR RESID 301:310 OR RESID 201:202 OR RESID 204:204 OR RESID 203:203 ) )A301 - 310
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -3:195 OR RESID 301:310 OR RESID 201:202 OR RESID 204:204 OR RESID 203:203 ) )A201 - 202
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -3:195 OR RESID 301:310 OR RESID 201:202 OR RESID 204:204 OR RESID 203:203 ) )A204
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID -3:195 OR RESID 301:310 OR RESID 201:202 OR RESID 204:204 OR RESID 203:203 ) )A203

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