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- PDB-5wb3: Crystal structure of the influenza virus PA endonuclease in compl... -

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Basic information

Entry
Database: PDB / ID: 5wb3
TitleCrystal structure of the influenza virus PA endonuclease in complex with inhibitor 10j (SRI-30026)
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 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-GYA / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 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 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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)24,0356
Polymers23,1481
Non-polymers8875
Water28816
1
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,14224
Polymers92,5934
Non-polymers3,54820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_885-x+3,-y+3,z1
crystal symmetry operation3_855-y+3,x,z1
crystal symmetry operation4_585y,-x+3,z1
Buried area6770 Å2
ΔGint-174 kcal/mol
Surface area31880 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-36 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.698, 90.698, 134.310
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
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GYA / 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(5,6-dimethoxy-2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-ox o-1,6-dihydropyrimidine-4-carboxamide / SRI-30026


Mass: 585.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29ClN4O6S / Feature type: SUBJECT OF INVESTIGATION
#5: 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.8, 1.0 M Ammonium Sulfate, 10 mM MnCl2, 10 mM MgCl2, 1% PVP K15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14550 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 53.35 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.024 / Rrim(I) all: 0.068 / Χ2: 1.287 / Net I/σ(I): 13 / Num. measured all: 113676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.287.81.070.7760.411.1481.035100
2.28-2.3780.7840.8650.2970.841.041100
2.37-2.487.90.5220.9340.1980.5581.095100
2.48-2.617.90.3640.9670.1390.391.134100
2.61-2.7780.2520.9790.0960.271.131100
2.77-2.997.90.1470.9930.0560.1571.248100
2.99-3.297.90.0930.9960.0350.11.435100
3.29-3.767.90.0680.9970.0250.0721.61100
3.76-4.747.70.0520.9980.0190.0551.53100
4.74-507.30.0330.9970.0140.0361.699.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→37.582 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.68
RfactorNum. reflection% reflection
Rfree0.2417 707 4.86 %
Rwork0.2152 --
obs0.2165 14541 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.55 Å2 / Biso mean: 77.8499 Å2 / Biso min: 47.3 Å2
Refinement stepCycle: final / Resolution: 2.203→37.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 52 16 1478
Biso mean--94.98 71.53 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041492
X-RAY DIFFRACTIONf_angle_d0.5832020
X-RAY DIFFRACTIONf_chiral_restr0.04212
X-RAY DIFFRACTIONf_plane_restr0.004259
X-RAY DIFFRACTIONf_dihedral_angle_d4.414896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2026-2.37270.33721400.286227022842
2.3727-2.61140.2581580.244126952853
2.6114-2.98910.25961390.234327392878
2.9891-3.76540.26181260.236527912917
3.7654-37.58790.221440.19229073051
Refinement TLS params.Method: refined / Origin x: 129.002 Å / Origin y: 111.7836 Å / Origin z: 286.5549 Å
111213212223313233
T0.8043 Å2-0.1289 Å20.3626 Å2-0.4186 Å20.0906 Å2--0.5815 Å2
L4.5236 °2-0.8934 °21.0387 °2-2.0104 °2-0.3431 °2--3.6755 °2
S0.1241 Å °-0.2837 Å °-0.3835 Å °0.3857 Å °-0.3754 Å °0.1943 Å °0.909 Å °-0.0107 Å °0.1567 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 195
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allD2 - 3
4X-RAY DIFFRACTION1allC1 - 16
5X-RAY DIFFRACTION1allE1

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