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- PDB-6vl3: The crystal structure of the 2009 H1N1 PA endonuclease mutant I38... -

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Basic information

Entry
Database: PDB / ID: 6vl3
TitleThe crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986436
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-R1D / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Jayaraman, S. / 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
DepositionJan 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4606
Polymers23,1361
Non-polymers1,3245
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.804, 89.804, 132.729
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 30 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-R1D / 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide


Mass: 449.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F3N3O5 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.89 Å3/Da / Density % sol: 57.46 % / Description: elongated
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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→45.88 Å / Num. obs: 7558 / % possible obs: 95.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.015 / Rrim(I) all: 0.03 / Χ2: 0.31 / Net I/σ(I): 16
Reflection shellResolution: 2.68→2.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2 / Num. unique obs: 1001 / CC1/2: 0.889 / Rpim(I) all: 0.177 / Rrim(I) all: 0.35 / Χ2: 0.31 / % possible all: 97.9

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Processing

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

5vpt


Resolution: 2.68→33.18 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.87
RfactorNum. reflection% reflection
Rfree0.2947 365 4.86 %
Rwork0.253 --
obs0.2551 7514 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.31 Å2 / Biso mean: 66.6514 Å2 / Biso min: 23.72 Å2
Refinement stepCycle: final / Resolution: 2.68→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 87 25 1537
Biso mean--95.86 54.58 -
Num. residues----179
LS refinement shellResolution: 2.68→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 3
RfactorNum. reflection% reflection
Rfree0.4736 120 -
Rwork0.376 2397 -
all-2517 -
obs--97 %

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