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- PDB-8dtw: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/C... -

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Basic information

Entry
Database: PDB / ID: 8dtw
TitleThe crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023036
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


viral translational frameshifting / viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
: / Hexa Vinylpyrrolidone K15 / Chem-TLR / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
#1: Journal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5808
Polymers23,1361
Non-polymers1,4447
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.554, 89.554, 133.963
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: i38t
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 6 types, 62 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TLR / 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-{[2-(trifluoromethyl)phenyl]methyl}-1,6-dihydropyrimidine-4-carboxamide


Mass: 448.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19F3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→74.45 Å / Num. obs: 11499 / % possible obs: 96.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 14.7
Reflection shellResolution: 2.33→2.41 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1142 / CC1/2: 0.873 / Rpim(I) all: 0.386

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.33→44.78 Å / SU ML: 0.4303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.0949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 602 5.24 %
Rwork0.2211 10895 -
obs0.2237 11497 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.93 Å2
Refinement stepCycle: LAST / Resolution: 2.33→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 86 55 1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171560
X-RAY DIFFRACTIONf_angle_d0.41712109
X-RAY DIFFRACTIONf_chiral_restr0.0371219
X-RAY DIFFRACTIONf_plane_restr0.0026266
X-RAY DIFFRACTIONf_dihedral_angle_d13.6036227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.560.3571760.31562730X-RAY DIFFRACTION98.28
2.56-2.940.30231450.27852716X-RAY DIFFRACTION97.38
2.94-3.70.32331400.24782750X-RAY DIFFRACTION96.66
3.7-44.780.24431410.19082699X-RAY DIFFRACTION90.3
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.740228432170.5494444456213.599143043450.4051113825010.7416255958398.209128029820.02907046642430.561605990416-0.4414143972480.0716660826114-0.1620602320770.3860044429790.6701603194380.2796791553860.1963593750090.758817522094-0.04347856577340.2448654153110.509574687435-0.02686690878360.75778162129334.924387826120.64843627447.34314966012
29.10673957509-1.689325254390.2197008803393.46954001398-0.2451284929715.139998976010.248894869554-0.409579189324-0.1510426523230.379021732735-0.318557146119-0.1898118431060.4815596675950.1337002014510.05556416757850.813391443066-0.03188729284850.1336913865580.5586625424950.211369456420.63558984893548.342867366821.218045323322.1964000266
39.24296505713-5.125736321673.2916561112.8921914192-1.988215902239.388295547240.27270317149-1.65735834826-1.58260807427-1.075530174420.5797788101870.8954728873850.718438494093-0.873139045875-1.027595559381.64375889207-0.1671124785290.2947764496560.9544258083260.2255286813581.0803040080834.52414212210.722934670327.5633563207
44.01287510748-0.5243180039212.988931957850.782105558240.2755095584995.38249907565-0.0268191947741-0.519757040362-0.2161345715530.256910587611-0.232818741010.1303501680030.347719652367-0.5547624936510.1609917079580.796058331254-0.206476811090.3107463315770.6489098680760.02443138505860.78078583118330.00548756921.895599493722.1765149214
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -3 through 50 )-3 - 501 - 54
22chain 'A' and (resid 51 through 126 )51 - 12655 - 111
33chain 'A' and (resid 127 through 137 )127 - 137112 - 122
44chain 'A' and (resid 138 through 195 )138 - 195123 - 180

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