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- PDB-6wij: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6wij
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease mutant I38T in complex with SJ000986448
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


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-U3A / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
CitationJournal: 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
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,5427
Polymers23,1361
Non-polymers1,4056
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.564, 89.564, 132.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein


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. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Gene: PA-X, PA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A481PFF5, UniProt: C6H0Y9

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Non-polymers , 5 types, 29 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-U3A / 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide


Mass: 434.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.15 Å3/Da / Density % sol: 60.94 % / Description: elongated rod.
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: 1.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.44→74.27 Å / Num. obs: 10430 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 67.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.047 / Rrim(I) all: 0.213 / Χ2: 0.95 / Net I/σ(I): 7.5
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1156 / CC1/2: 0.866 / Rpim(I) all: 0.319 / Rrim(I) all: 1.499 / Χ2: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.44→74.27 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.51
Details: data merged from 4 independant crystals with CCP4/BLEND then scaled with AIMLESS.
RfactorNum. reflection% reflection
Rfree0.2645 530 5.08 %
Rwork0.2148 --
obs0.2171 10430 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.25 Å2 / Biso mean: 86.8367 Å2 / Biso min: 45.58 Å2
Refinement stepCycle: final / Resolution: 2.44→74.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 77 23 1520
Biso mean--125.51 83.15 -
Num. residues----180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.44-2.690.31211670.266723812548
2.69-3.070.33981020.265124632565
3.07-3.870.28071340.224524502584
3.88-74.270.23691270.195826062733
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)
14.7261.2288-1.44253.08333.45816.1967-0.093-0.3632-0.18681.63440.66580.28830.86690.4486-0.42960.7969-0.0336-0.03060.80350.20350.6985-22.6892-28.2188-3.0364
23.28140.72882.80512.8156-0.6393.44421.07720.4497-0.32971.6174-0.9791-0.42810.66780.6344-0.0430.91270.1111-0.05570.94970.15470.7569-20.8223-40.8419-5.0112
34.89712.87733.29067.27490.42333.10470.41730.0161-1.3695-0.02750.5078-0.76160.32222.136-0.94890.92120.3217-0.37211.51080.17990.9754-12.0496-36.5908-3.1544
44.1916-0.41323.49963.11514.04848.9615-0.1675-0.32090.33310.1993-0.13480.51530.8218-0.23710.17870.5147-0.05840.06530.52510.19840.7067-23.3869-36.214-14.4964
58.08720.5348-0.79347.848-2.93563.6006-0.67380.4443-0.7112-0.12780.23210.42910.26910.81430.59030.67860.11250.19240.73090.17710.7019-23.0538-52.5443-19.1501
64.5409-1.2552-1.15434.95820.96133.0839-0.52980.79080.1115-0.94720.3982-0.3816-0.44320.7492-0.03450.5691-0.09940.16620.80830.19950.5852-18.9851-44.6326-24.8223
76.0967-3.18244.27466.2342-1.08673.29220.8323-0.56242.4186-0.7267-0.4359-2.140.3639-0.7854-0.08330.9229-0.29740.27421.40490.10090.931-10.8804-35.2193-27.3426
84.968-2.3331-2.02645.59755.29875.3276-0.92290.2397-0.03850.02751.32590.26841.0378-0.6887-0.52970.7797-0.13610.19440.82160.22820.7093-17.4996-40.1491-28.1515
92.8724-1.3820.72199.32525.70444.39510.38570.47010.2364-0.3106-0.5567-0.5554-0.0383-0.28930.24390.7583-0.10640.06421.15820.26820.8171-23.1193-34.2144-30.1759
100.7908-1.08311.26597.76644.16077.9665-0.3448-0.15290.22610.11710.1227-0.1216-1.04350.61790.08770.6876-0.3168-0.07580.7420.35510.7695-23.1832-24.9792-16.674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 10 )A-3 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 23 )A11 - 23
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 31 )A24 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 51 )A32 - 51
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 79 )A52 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 107 )A80 - 107
7X-RAY DIFFRACTION7chain 'A' and (resid 108 through 119 )A108 - 119
8X-RAY DIFFRACTION8chain 'A' and (resid 120 through 130 )A120 - 130
9X-RAY DIFFRACTION9chain 'A' and (resid 131 through 145 )A131 - 145
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 176 )A146 - 176

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