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- PDB-5w44: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5w44
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 7a (SRI-29770)
ComponentsPolymerase acidic protein
Keywordshydrolase/hydrolase inhibitor / nuclease / transcription / cap-snatching / virus / 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-GY6 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6525
Polymers21,0481
Non-polymers6044
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein purifies as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.111, 74.111, 127.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21048.053 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 62 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GY6 / 2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide


Mass: 501.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22Cl2N4O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 30% PEG 4000, 0.2 M MgCl2, 2 mM MnCl2

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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: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12718 / % possible obs: 99.7 % / Redundancy: 16.5 % / Biso Wilson estimate: 36.87 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.024 / Rrim(I) all: 0.097 / Χ2: 1.018 / Net I/σ(I): 7.2 / Num. measured all: 210115
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1811.60.62412120.9270.1780.650.60597.6
2.18-2.2614.90.5112100.9640.1320.5270.64399.8
2.26-2.3717.30.40512400.9820.0990.4170.68599.8
2.37-2.4917.80.32712460.9870.0790.3370.732100
2.49-2.6517.80.23512630.9930.0570.2420.855100
2.65-2.8517.80.17912600.9940.0440.1851.004100
2.85-3.1417.70.12812570.9960.0310.1321.211100
3.14-3.5917.50.09612830.9970.0230.0981.404100
3.59-4.5217.20.07713090.9990.0190.081.48899.9
4.52-5015.60.0514380.9990.0130.0521.29899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.22 Å42.62 Å
Translation5.22 Å42.62 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DES

5des


Resolution: 2.1→35.591 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 757 5.97 %
Rwork0.1928 11922 -
obs0.1947 12679 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.76 Å2 / Biso mean: 51.6845 Å2 / Biso min: 24.21 Å2
Refinement stepCycle: final / Resolution: 2.1→35.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 59 58 1560
Biso mean--57.68 49.73 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051510
X-RAY DIFFRACTIONf_angle_d0.6252037
X-RAY DIFFRACTIONf_chiral_restr0.046215
X-RAY DIFFRACTIONf_plane_restr0.004263
X-RAY DIFFRACTIONf_dihedral_angle_d16.351919
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 (%)
2.0997-2.26180.24011400.20352257239797
2.2618-2.48930.26951380.207423522490100
2.4893-2.84940.26431530.223692522100
2.8494-3.58940.24311440.201223962540100
3.5894-35.59570.20021820.182725482730100
Refinement TLS params.Method: refined / Origin x: -14.361 Å / Origin y: 75.9972 Å / Origin z: 14.0938 Å
111213212223313233
T0.3656 Å20.0166 Å20.0876 Å2-0.2204 Å2-0.0373 Å2--0.4094 Å2
L1.5974 °2-0.0914 °2-0.1739 °2-3.158 °20.6996 °2--3.295 °2
S-0.0939 Å °0.1018 Å °-0.4228 Å °-0.2025 Å °-0.084 Å °-0.2374 Å °0.4884 Å °0.0776 Å °0.1333 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 178
2X-RAY DIFFRACTION1allB301
3X-RAY DIFFRACTION1allS5 - 72
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allE1

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