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- PDB-5wa6: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5wa6
TitleCrystal structure of the influenza virus PA endonuclease in complex with an inhibitor - SRI-30007
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Virus / Nuclease / Transcription / Cap-snatching / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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-KU7 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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.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)23,7554
Polymers23,1481
Non-polymers6063
Water1448
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 area140 Å2
ΔGint-7 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.563, 90.563, 135.167
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-KU7 / 2-{(2S)-1-[(2-fluorophenoxy)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4-carboxamide


Mass: 496.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25FN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 13745 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 57.79 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Χ2: 1.281 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.3371.1260.6880.4481.2150.87699.4
2.33-2.427.90.8780.8550.3320.940.882100
2.42-2.5380.6170.9210.2310.660.948100
2.53-2.678.10.4340.9570.1620.4640.937100
2.67-2.8380.3060.9720.1140.3270.97100
2.83-3.0580.1630.9930.0610.1741.071100
3.05-3.3680.0950.9960.0360.1021.314100
3.36-3.857.90.0670.9970.0250.0721.818100
3.85-4.857.80.0660.9960.0250.0712.312100
4.85-507.40.0320.9990.0130.0351.60799.7

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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: 2.25→38.797 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.56
RfactorNum. reflection% reflection
Rfree0.2535 737 5.37 %
Rwork0.2307 --
obs0.2321 13733 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.71 Å2 / Biso mean: 91.5786 Å2 / Biso min: 53.87 Å2
Refinement stepCycle: final / Resolution: 2.25→38.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 38 8 1453
Biso mean--102.91 82.39 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031476
X-RAY DIFFRACTIONf_angle_d0.5931993
X-RAY DIFFRACTIONf_chiral_restr0.04211
X-RAY DIFFRACTIONf_plane_restr0.004258
X-RAY DIFFRACTIONf_dihedral_angle_d3.637889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2487-2.42230.31881300.288625452675
2.4223-2.6660.29511430.252825802723
2.666-3.05160.26541620.259725432705
3.0516-3.84420.26861340.255626092743
3.8442-38.80260.23521680.20727192887
Refinement TLS params.Method: refined / Origin x: 490.908 Å / Origin y: 202.292 Å / Origin z: 558.793 Å
111213212223313233
T1.0251 Å2-0.1443 Å20.4617 Å2-0.6365 Å20.1221 Å2--0.6975 Å2
L3.8983 °2-0.3477 °20.2297 °2-1.7595 °2-0.3266 °2--2.461 °2
S0.0455 Å °-0.6157 Å °-0.5015 Å °0.6827 Å °-0.4818 Å °0.1653 Å °0.9833 Å °-0.1313 Å °0.3089 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:202 OR RESID 302:304 OR RESID 203:203 ) )A-2 - 176
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:202 OR RESID 302:304 OR RESID 203:203 ) )A201 - 202
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:202 OR RESID 302:304 OR RESID 203:203 ) )A302 - 304
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:202 OR RESID 302:304 OR RESID 203:203 ) )A203

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