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- PDB-6e3m: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 6e3m
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 6-(3-carboxyphenyl)-3-hydroxy-4-oxo-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 / 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-HOG / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 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 / 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)22,9165
Polymers22,4691
Non-polymers4474
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-5 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.459, 75.459, 120.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-903-

EDO

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HOG / 6-(3-carboxyphenyl)-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Mass: 275.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.65→44.35 Å / Num. obs: 6352 / % possible obs: 99.8 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.06 / Net I/σ(I): 40
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 803 / Rpim(I) all: 0.205 / Rrim(I) all: 0.696 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.65→44.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.067 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26436 523 8.3 %RANDOM
Rwork0.19226 ---
obs0.19831 5800 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.65→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 26 25 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141529
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171354
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.6842049
X-RAY DIFFRACTIONr_angle_other_deg0.9361.6443175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49921.18393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89415287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5171514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
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_it4.5165.831705
X-RAY DIFFRACTIONr_mcbond_other4.5055.827704
X-RAY DIFFRACTIONr_mcangle_it6.2728.725876
X-RAY DIFFRACTIONr_mcangle_other6.278.731877
X-RAY DIFFRACTIONr_scbond_it5.7216.545824
X-RAY DIFFRACTIONr_scbond_other5.6876.528816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6599.5531164
X-RAY DIFFRACTIONr_long_range_B_refined10.5566.8671766
X-RAY DIFFRACTIONr_long_range_B_other10.48566.7661752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.654→2.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 37 -
Rwork0.254 408 -
obs--98.45 %

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