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- PDB-6e3n: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 6e3n
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-4-oxo-6-(o-tolyl)-1,4-dihydropyridine-2-carboxylic acid
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PA endonuclease / inhibitor / influenza / H1N1 / 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 / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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-HNS / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / Resolution: 3.19 Å
AuthorsMorrison, C.N. / Dick, B.L. / Credille, C.V. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098435 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease.
Authors: Credille, C.V. / Morrison, C.N. / Stokes, R.W. / Dick, B.L. / Feng, Y. / Sun, J. / Chen, Y. / Cohen, S.M.
History
DepositionJul 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)22,8244
Polymers22,4691
Non-polymers3553
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-7 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.481, 74.481, 119.189
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 22468.666 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198)
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 BL21 (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-HNS / 3-hydroxy-6-(2-methylphenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Mass: 245.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.19→37.24 Å / Num. obs: 3603 / % possible obs: 99.7 % / Redundancy: 18.95 % / Rmerge(I) obs: 0.1828 / Net I/σ(I): 13.83
Reflection shellResolution: 3.19→3.29 Å / Redundancy: 12.97 % / Rmerge(I) obs: 0.4231 / Mean I/σ(I) obs: 3.27 / Num. unique obs: 286 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
APEXAPEX3data reduction
APEXAPEX3data scaling
PHASERphasing
Cootmodel building
RefinementResolution: 3.19→37.24 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.825 / SU B: 26.269 / SU ML: 0.437 / Cross valid method: THROUGHOUT / ESU R Free: 0.685 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28475 615 17.2 %RANDOM
Rwork0.19493 ---
obs0.20973 2962 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.424 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 3.19→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 20 1 1478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0141505
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171335
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.6812020
X-RAY DIFFRACTIONr_angle_other_deg0.8241.6443129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50321.42991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94415281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.851513
X-RAY DIFFRACTIONr_chiral_restr0.0540.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3494.067697
X-RAY DIFFRACTIONr_mcbond_other2.3464.067696
X-RAY DIFFRACTIONr_mcangle_it3.9046.083866
X-RAY DIFFRACTIONr_mcangle_other3.9026.084867
X-RAY DIFFRACTIONr_scbond_it2.5044.278806
X-RAY DIFFRACTIONr_scbond_other2.5034.277807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1476.3061155
X-RAY DIFFRACTIONr_long_range_B_refined6.26545.8941751
X-RAY DIFFRACTIONr_long_range_B_other6.26345.8841752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.195→3.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 43 -
Rwork0.244 201 -
obs--98.79 %

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