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- PDB-5if5: Crystal structure of polymerase acid protein (PA) from Influenza ... -

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Basic information

Entry
Database: PDB / ID: 5if5
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to EBSI-39 (2,3-dichlorophenyl)methanol
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / structural genomics / flu / fragment screening / 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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / 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
(2,3-dichlorophenyl)methanol / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)53,5386
Polymers53,0971
Non-polymers4415
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint12 kcal/mol
Surface area19730 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,07612
Polymers106,1932
Non-polymers88310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area5210 Å2
ΔGint11 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 68.430, 395.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-6B0 / (2,3-dichlorophenyl)methanol


Mass: 177.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6Cl2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe distance between Residue A GLU 677 and Residue A PHE 681 is 20.95 Angstrom despite the fact ...The distance between Residue A GLU 677 and Residue A PHE 681 is 20.95 Angstrom despite the fact that there are only 3 residues (not enough sequence) to cover the gap region. One possibility for that is some domain swapping for the last two helices (note that E677 is closer to the symmetry related F681). Another possibility is that the protein is clipped. There is a bit of a doublet in the SDS PAGE of this protein.

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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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mg/mL protein against Morpheus D10 with 10% PEG 8000, 20% EG, 0.02 M each alcohol, 0.1 M bicine/Trisma base pH 8.5, crystal tracking ID 263964d10, 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: 2.25→50 Å / Num. obs: 27497 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.310.4914.151100
2.31-2.370.454.641100
2.37-2.440.3735.271100
2.44-2.520.2946.491100
2.52-2.60.2727.051100
2.6-2.690.2317.961100
2.69-2.790.1929.361100
2.79-2.90.15410.91100
2.9-3.030.1312.721100
3.03-3.180.1114.651100
3.18-3.350.09916.191100
3.35-3.560.08519.33199.9
3.56-3.80.07920.631100
3.8-4.110.07322.28199.9
4.11-4.50.07123.53199.7
4.5-5.030.07123.671100
5.03-5.810.06922.99199.8
5.81-7.120.07322.49199.7
7.12-10.060.0724.11199.5
10.06-47.4360.06722.49196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.436 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1322 4.81 %
Rwork0.1755 --
obs0.177 27491 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→47.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 26 145 3334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073278
X-RAY DIFFRACTIONf_angle_d0.8524429
X-RAY DIFFRACTIONf_dihedral_angle_d13.0741995
X-RAY DIFFRACTIONf_chiral_restr0.045496
X-RAY DIFFRACTIONf_plane_restr0.005561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.24941420.19662828X-RAY DIFFRACTION100
2.3401-2.44660.25931300.19232862X-RAY DIFFRACTION100
2.4466-2.57550.18861410.17162813X-RAY DIFFRACTION100
2.5755-2.73690.21711660.17472842X-RAY DIFFRACTION100
2.7369-2.94820.22011500.17462828X-RAY DIFFRACTION100
2.9482-3.24480.23071210.1732912X-RAY DIFFRACTION100
3.2448-3.71420.20551530.17062912X-RAY DIFFRACTION100
3.7142-4.67880.1691430.16052976X-RAY DIFFRACTION100
4.6788-47.44610.21631760.18743196X-RAY DIFFRACTION99
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)
10.69730.64780.84952.0482-0.64751.8521-0.0287-0.0647-0.0543-0.1409-0.082-0.15330.0328-0.08520.10780.29530.08650.06560.26440.06640.293-15.86-32.140950.9933
22.1214-0.2271.23922.42860.06232.8319-0.0076-0.3076-0.16310.15690.1350.20980.4527-0.273-0.08560.40730.0630.0720.22260.08830.2929-19.5057-45.775162.3222
30.6878-1.01170.54292.0504-0.90662.2982-0.2445-0.0635-0.02620.15260.0595-0.08690.0901-0.0430.21550.28550.08040.02310.24510.02480.2918-13.6902-34.540658.9629
40.7494-0.29350.04721.7165-0.53042.7708-0.02870.02670.13350.00020.0752-0.0119-0.3188-0.2646-0.01330.25650.11330.06870.24130.0440.2592-19.4196-25.05251.5274
50.67040.0278-0.50661.322-0.74171.84430.00570.25780.2666-0.1559-0.0376-0.2309-0.84830.14640.13880.61460.00390.09590.33790.09180.424-7.9799-13.121235.7668
62.87342.2256-1.62532.1036-1.18330.9337-0.3026-0.00540.12350.0063-0.0931-0.77410.1180.90440.23420.3880.00380.07310.54440.17730.60866.2916-21.076440.0961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 313 )
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 415 )
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 603 )
5X-RAY DIFFRACTION5chain 'A' and (resid 604 through 675 )
6X-RAY DIFFRACTION6chain 'A' and (resid 676 through 713 )

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