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

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Basic information

Entry
Database: PDB / ID: 5ieq
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-747 1-(4-chlorophenyl)-1H-imidazole
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / structural genomics / fragment screening / STD NMR / fragments of life / flu / 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
1-(4-CHLOROPHENYL)-1H-IMIDAZOLE / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.1Mar 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)53,3533
Polymers53,0971
Non-polymers2572
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint1 kcal/mol
Surface area19350 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7076
Polymers106,1932
Non-polymers5144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area4290 Å2
ΔGint-10 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.370, 69.370, 397.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-1CI / 1-(4-CHLOROPHENYL)-1H-IMIDAZOLE


Mass: 178.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClN2
#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.: 195 / 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: 52.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mg/mL protein against Morpheus H6, 10% PEG 8000, 20% EG, 0.02 M each amino acid, 0.1 M MOPS/Hepes pH 7.5, crystal ID 254835h6, unique puck ID fhx2-7

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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: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→47.941 Å / Num. obs: 30171 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.260.5783.521100
2.26-2.320.4674.311100
2.32-2.390.4035.061100
2.39-2.460.3246.1199.9
2.46-2.540.2587.521100
2.54-2.630.2288.44199.9
2.63-2.730.1919.88199.9
2.73-2.840.14712.26199.9
2.84-2.970.11715.11199.9
2.97-3.110.09318.81199.9
3.11-3.280.07821.5199.9
3.28-3.480.06326.29199.7
3.48-3.720.05331199.1
3.72-4.020.04733.56199.3
4.02-4.40.04337.4199.1
4.4-4.920.0438.75198.8
4.92-5.680.0436.96198.8
5.68-6.960.03935.88198.3
6.96-9.840.03340.4197.9
9.84-47.9410.03138.73195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.941 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.2213 2019 6.69 %
Rwork0.1746 --
obs0.1778 30169 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.89 Å2 / Biso mean: 43.6042 Å2 / Biso min: 15.02 Å2
Refinement stepCycle: final / Resolution: 2.2→47.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 16 195 3348
Biso mean--47.75 44.88 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083250
X-RAY DIFFRACTIONf_angle_d0.8934405
X-RAY DIFFRACTIONf_chiral_restr0.048493
X-RAY DIFFRACTIONf_plane_restr0.005563
X-RAY DIFFRACTIONf_dihedral_angle_d12.0491970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2550.24851500.188819552105100
2.255-2.3160.23791280.18420052133100
2.316-2.38420.25331470.175919282075100
2.3842-2.46110.21881630.176519372100100
2.4611-2.54910.23041380.175419702108100
2.5491-2.65110.24531200.186619922112100
2.6511-2.77180.25181270.188320042131100
2.7718-2.91790.27521380.185119892127100
2.9179-3.10070.22681470.182719762123100
3.1007-3.340.23291280.183320522180100
3.34-3.6760.21341280.162220402168100
3.676-4.20770.17371630.15621998216199
4.2077-5.30020.20451650.15032078224399
5.3002-47.95190.2341770.1982226240398
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)
10.2076-0.04260.46070.9603-0.31540.967-0.00870.02760.1059-0.1836-0.1082-0.1742-0.0563-0.2182-0.01550.25610.10990.07850.21540.07420.2704-16.1664-30.585750.1981
20.0710.034-0.18840.2439-0.03540.5792-0.0451-0.0782-0.131-0.03630.06570.09560.3484-0.2201-0.00420.33470.0770.05850.25010.07310.3178-22.8369-43.086858.7107
30.20240.20430.16190.20060.04260.4443-0.298-0.10060.06320.3160.13330.11210.0706-0.3112-0.05950.30360.14670.07890.24580.06920.2786-24.5149-40.375369.3109
41.0692-0.03070.49220.58140.06710.2485-0.42690.3168-0.0512-0.0295-0.057-0.37860.09650.3445-0.39070.30070.24860.11550.14890.0750.3126-7.4386-33.869152.7513
50.47990.1033-0.01331.2064-0.47091.8114-0.0090.00470.0774-0.04170.0607-0.0142-0.234-0.26030.01110.23990.160.07190.14390.05170.1873-20.338-24.815552.0021
60.49250.1068-0.53320.4187-0.02530.4271-0.01130.17970.1283-0.1725-0.2182-0.3762-0.42440.31380.01460.42890.00870.09170.32150.17620.3922-4.5626-16.102138.0576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 302 )A265 - 302
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 330 )A303 - 330
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 363 )A331 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 415 )A364 - 415
5X-RAY DIFFRACTION5chain 'A' and (resid 416 through 602 )A416 - 602
6X-RAY DIFFRACTION6chain 'A' and (resid 603 through 713 )A603 - 713

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