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- PDB-6wj4: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6wj4
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease wild type in complex with SJ000986448
ComponentsPolymerase acidic protein
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-U3A / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 11, 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)24,5547
Polymers23,1481
Non-polymers1,4056
Water52229
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,42956
Polymers185,1878
Non-polymers11,24248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area18230 Å2
ΔGint-337 kcal/mol
Surface area59780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 90.090, 132.141
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: 23148.344 Da / Num. of mol.: 1
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, 35 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.: 29 / 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: 57.52 %
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: 2.55→74.44 Å / Num. obs: 9099 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.065 / Χ2: 0.4 / Net I/σ(I): 16.1
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1072 / CC1/2: 0.879 / Rpim(I) all: 0.329 / Rrim(I) all: 0.911 / Χ2: 0.38 / % possible all: 98.4

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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: 2.55→63.7 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.03
RfactorNum. reflection% reflection
Rfree0.2732 443 4.87 %
Rwork0.2282 --
obs0.2305 9095 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.57 Å2 / Biso mean: 82.2965 Å2 / Biso min: 41.92 Å2
Refinement stepCycle: final / Resolution: 2.55→63.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 77 29 1515
Biso mean--124.4 70.88 -
Num. residues----179
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 (%)
2.55-2.920.42571310.33032794292598
2.92-3.680.31491490.26212859300899
3.68-63.70.23951630.1992999316299
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)
17.73892.9743-1.70554.31392.78354.115-0.238-0.15330.65141.63790.70710.89530.19050.8499-0.67230.8658-0.0532-0.07010.90660.14530.7441-23.849-29.011-3.384
29.77521.64452.67377.55264.20382.7933-0.141-0.2127-0.64210.77120.1006-0.46881.05861.1380.17810.59610.0547-0.02250.82270.23870.644-18.097-39.877-4.335
32.4469-0.35993.72334.62162.53427.8069-0.02850.06650.31580.3203-0.2610.12960.7191-0.12360.150.567-0.0880.1650.72340.26010.6986-25.335-41.444-16.459
48.2890.53943.55156.75362.27032.3386-0.5550.2643-0.3231-0.39660.486-1.01210.47071.67070.09490.79010.07730.27510.80420.13890.7656-19.053-56.763-18.855
50.96870.02880.18192.06310.85542.63090.01630.5075-0.007-0.8672-0.3292-0.27660.0390.08680.1820.6461-0.04420.23420.63880.15010.7349-19.347-45.27-24.884
69.5171-6.52740.42218.90663.12986.05370.4658-0.69650.7743-0.453-0.1308-1.07620.5833-0.1758-0.30460.77-0.27450.23781.66460.10510.8065-10.933-35.659-27.139
73.599-0.6244-1.61768.16333.18757.2841-0.10640.33970.1924-0.3157-0.0747-0.1355-0.30090.40140.11570.4437-0.12070.01890.64210.32680.563-22.399-30.624-22.147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:10 )A-2 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 11:31 )A11 - 31
3X-RAY DIFFRACTION3( CHAIN A AND RESID 32:53 )A32 - 53
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:79 )A73 - 79
5X-RAY DIFFRACTION5( CHAIN A AND RESID 80:107 )A80 - 107
6X-RAY DIFFRACTION6( CHAIN A AND RESID 108:119 )A108 - 119
7X-RAY DIFFRACTION7( CHAIN A AND RESID 120:176 )A120 - 176

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