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- PDB-5w7u: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5w7u
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 8f (SRI-29928)
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 / 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-GY8 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 20, 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7734
Polymers23,1481
Non-polymers6243
Water19811
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 area150 Å2
ΔGint-7 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.746, 90.746, 135.256
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
Mutation: Loop residues 51-72 are replaced by a GGS linker, N-terminal residues from the His-tag
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-GY8 / 2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropy rimidine-4-carboxamide / SRI-29928


Mass: 514.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21Cl2N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
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-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 7, 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: 14588 / % possible obs: 98.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 56.88 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.017 / Rrim(I) all: 0.054 / Χ2: 0.942 / Net I/σ(I): 12.5 / Num. measured all: 135750
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.90.7080.8650.270.760.67791.8
2.28-2.378.30.6530.9210.2370.6960.74299.8
2.37-2.489.30.4810.9670.1650.5090.777100
2.48-2.619.90.3540.9780.1180.3730.781100
2.61-2.77100.240.990.080.2540.822100
2.77-2.99100.1360.9950.0450.1440.895100
2.99-3.299.90.0760.9980.0250.0810.976100
3.29-3.769.90.0530.9990.0180.0561.143100
3.76-4.749.80.040.9990.0140.0431.139100
4.74-508.90.0310.9990.0110.0331.32897.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.084 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.13
RfactorNum. reflection% reflection
Rfree0.2443 689 4.73 %
Rwork0.2185 --
obs0.2197 14582 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.21 Å2 / Biso mean: 89.9716 Å2 / Biso min: 52.48 Å2
Refinement stepCycle: final / Resolution: 2.2→32.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 37 11 1447
Biso mean--99.46 77.48 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081468
X-RAY DIFFRACTIONf_angle_d0.9021985
X-RAY DIFFRACTIONf_chiral_restr0.047210
X-RAY DIFFRACTIONf_plane_restr0.005255
X-RAY DIFFRACTIONf_dihedral_angle_d4.781884
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 (%)
2.1986-2.36830.32771350.29652617275296
2.3683-2.60660.31251480.264427542902100
2.6066-2.98350.28561520.25127612913100
2.9835-3.7580.30361120.237928502962100
3.758-32.0870.20371420.19362911305399
Refinement TLS params.Method: refined / Origin x: 128.6361 Å / Origin y: 111.9441 Å / Origin z: 288.451 Å
111213212223313233
T0.9751 Å2-0.1998 Å20.3849 Å2-0.5552 Å20.0933 Å2--0.7708 Å2
L3.4228 °2-1.374 °20.4619 °2-2.1321 °2-0.0019 °2--2.7751 °2
S-0.0793 Å °-0.4622 Å °-0.3015 Å °0.4674 Å °-0.3056 Å °0.2173 Å °0.9326 Å °-0.2262 Å °0.2382 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq -3:176) or (chain B and resseq 1:1) or (chain B and resseq 2:2) or (chain D and resseq 1:1)A-3 - 176
2X-RAY DIFFRACTION1(chain A and resseq -3:176) or (chain B and resseq 1:1) or (chain B and resseq 2:2) or (chain D and resseq 1:1)B1
3X-RAY DIFFRACTION1(chain A and resseq -3:176) or (chain B and resseq 1:1) or (chain B and resseq 2:2) or (chain D and resseq 1:1)B2
4X-RAY DIFFRACTION1(chain A and resseq -3:176) or (chain B and resseq 1:1) or (chain B and resseq 2:2) or (chain D and resseq 1:1)D1

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