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

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Basic information

Entry
Database: PDB / ID: 5wct
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 6c (SRI-29775)
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 / 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-GY4 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionJul 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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)22,4584
Polymers21,9701
Non-polymers4883
Water28816
1
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9168
Polymers43,9402
Non-polymers9756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1400 Å2
ΔGint-29 kcal/mol
Surface area17590 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.561, 74.561, 125.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Polymerase acidic protein


Mass: 21970.160 Da / Num. of mol.: 1
Mutation: Loop 51-72 is replaced a GGS linker, C-terminal has residual 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: pET52b / 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-GY4 / 2-{(2S)-1-[(4-chlorophenyl)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid / SRI-29775


Mass: 377.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 M LiCl, 0.1 M Na-Acetate, 24% PEG 6000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9479 / % possible obs: 97.6 % / Redundancy: 16.5 % / Biso Wilson estimate: 58.03 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.027 / Rrim(I) all: 0.111 / Χ2: 1.913 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.38150.990.8120.2521.0240.94688.7
2.38-2.4815.60.7990.8780.2010.8251.03795.7
2.48-2.59160.6780.8870.170.71.10199.4
2.59-2.7316.80.4910.950.1220.5071.32499.6
2.73-2.916.80.3710.9730.0920.3831.54699.6
2.9-3.1216.80.2540.9850.0630.2622.17699.7
3.12-3.4417.10.1840.9930.0460.1892.53699.6
3.44-3.9317.40.1190.9960.0290.1232.899.4
3.93-4.9517.30.0870.9970.0210.092.73298.5
4.95-5015.60.0660.9980.0180.0692.40796.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.023 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.16
RfactorNum. reflection% reflection
Rfree0.2549 460 4.86 %
Rwork0.2188 --
obs0.2206 9470 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.78 Å2 / Biso mean: 86.736 Å2 / Biso min: 38.48 Å2
Refinement stepCycle: final / Resolution: 2.3→35.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 28 16 1445
Biso mean--72.2 67.75 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081459
X-RAY DIFFRACTIONf_angle_d0.8831972
X-RAY DIFFRACTIONf_chiral_restr0.048212
X-RAY DIFFRACTIONf_plane_restr0.006254
X-RAY DIFFRACTIONf_dihedral_angle_d3.889879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2973-2.62960.40371310.28482801293293
2.6296-3.31260.32371640.290830203184100
3.3126-35.02680.22331650.19133189335499
Refinement TLS params.Method: refined / Origin x: 21.7678 Å / Origin y: 13.6567 Å / Origin z: 7.0103 Å
111213212223313233
T0.552 Å20.1696 Å20.1009 Å2-0.5054 Å2-0.0484 Å2--0.7027 Å2
L2.6878 °2-0.4001 °2-0.6169 °2-1.4269 °20.1718 °2--3.6284 °2
S0.0739 Å °-0.2482 Å °0.6335 Å °0.1905 Å °-0.0056 Å °0.4259 Å °-0.7506 Å °-0.8226 Å °-0.0259 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 196
2X-RAY DIFFRACTION1allB201 - 202
3X-RAY DIFFRACTION1allC1 - 25
4X-RAY DIFFRACTION1allD1

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