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- PDB-5if7: Crystal structure of polymerase acid protein (PA) from Influenza ... -

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Basic information

Entry
Database: PDB / ID: 5if7
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-279 N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / structural genomics / flu / fragment screening / STD NMR / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Chem-6AY / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA
Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)53,4493
Polymers53,0971
Non-polymers3522
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area19130 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8976
Polymers106,1932
Non-polymers7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3050 Å2
ΔGint-7 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.210, 69.210, 399.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-945-

HOH

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 53096.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659
#2: Chemical ChemComp-6AY / N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 273.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12ClN5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mg/mL protein against Morpheus screen condition H6 10% PEG 8000, 20% EG, 0.02 M each amino acid, 0.1 M MOPS/Hepes pH 7.5, unique puck ID pyl5-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→44.546 Å / Num. obs: 15474 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.65-2.720.5784.33190
2.72-2.790.4165.77190.1
2.79-2.870.3267.25189.8
2.87-2.960.2659189.4
2.96-3.060.21510.78189.4
3.06-3.170.16913.21189.3
3.17-3.290.13916.14188.4
3.29-3.420.10919.24188.8
3.42-3.570.08723.66187.3
3.57-3.750.08124.77188
3.75-3.950.06429.89187.2
3.95-4.190.05634.38186.8
4.19-4.480.0537.72186.2
4.48-4.840.04839.72186.1
4.84-5.30.04938.68185.3
5.3-5.930.05435.22184.5
5.93-6.840.04938.29183.6
6.84-8.380.04143.86183
8.38-11.850.03747.92181.5
11.85-44.5460.03943.35177.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUJ

4iuj


Resolution: 2.65→44.546 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2409 1593 10.3 %
Rwork0.1832 --
obs0.1892 15470 87.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.93 Å2 / Biso mean: 52.8644 Å2 / Biso min: 22.24 Å2
Refinement stepCycle: final / Resolution: 2.65→44.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 23 46 3151
Biso mean--103.77 41.48 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073189
X-RAY DIFFRACTIONf_angle_d0.8284325
X-RAY DIFFRACTIONf_chiral_restr0.047487
X-RAY DIFFRACTIONf_plane_restr0.005551
X-RAY DIFFRACTIONf_dihedral_angle_d12.3681922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.73560.36741360.25941253138990
2.7356-2.83330.27191530.21811221137490
2.8333-2.94680.24921360.20161264140090
2.9468-3.08080.271610.18861234139589
3.0808-3.24320.26221410.20451260140189
3.2432-3.44630.27711470.1991257140489
3.4463-3.71230.22551380.17061237137588
3.7123-4.08570.2151450.1551270141587
4.0857-4.67630.18281400.14561259139986
4.6763-5.88950.24521420.18671275141785
5.8895-44.55240.2411540.19361347150182
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)
10.21760.07690.7792.8409-1.09433.28440.1901-0.04870.1689-0.1913-0.2431-0.01070.0872-0.3131-0.05750.37070.13740.0960.28910.09020.397-19.0738-31.770753.2581
21.3386-0.2039-0.13042.5864-0.59252.85060.02470.20350.1267-0.17080.07320.0773-0.2068-0.2394-0.03860.3510.17070.12110.29160.0870.2911-18.7485-27.344652.5214
32.75111.5478-1.54881.4081-0.76742.1148-0.2591-0.27860.0918-0.4253-0.2949-0.7427-0.25240.92830.30660.6113-0.02920.20360.54660.29490.65534.4294-17.543940.5682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 267 through 312 )A267 - 312
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 652 )A313 - 652
3X-RAY DIFFRACTION3chain 'A' and (resid 653 through 713 )A653 - 713

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