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- PDB-5if8: Crystal structure of polymerase acid protein (PA) from Influenza ... -

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Basic information

Entry
Database: PDB / ID: 5if8
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-2643 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-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 / 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
Chem-6AX / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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)53,5746
Polymers53,0971
Non-polymers4775
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-4 kcal/mol
Surface area19240 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,14812
Polymers106,1932
Non-polymers95510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area5060 Å2
ΔGint-13 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.780, 68.780, 396.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 102 molecules

#2: Chemical ChemComp-6AX / 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine


Mass: 209.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8ClN3O
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mg/mL protein against Morpheus screen condition A2 10% PEG 8000, 20% EG, 0.03 M each divalent cation, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 254988a2, unique puck ID wbm4-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.99985 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.3→41.025 Å / Num. obs: 25953 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.5043.941100
2.36-2.420.4334.531100
2.42-2.490.3285.951100
2.49-2.570.2627.571100
2.57-2.660.2428.151100
2.66-2.750.18910.61199.9
2.75-2.850.13114.291100
2.85-2.970.10717.851100
2.97-3.10.07524.071100
3.1-3.250.06128.441100
3.25-3.430.04836.391100
3.43-3.640.03746.041100
3.64-3.890.03153.671100
3.89-4.20.02463.44199.9
4.2-4.60.02271.92199.9
4.6-5.140.01975.81100
5.14-5.940.0270.84199.9
5.94-7.270.01872.69199.9
7.27-10.290.01682.27196.8
10.29-41.0250.01776.11181

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.3→41.025 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.2315 1230 4.74 %
Rwork0.1823 --
obs0.1846 25953 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.03 Å2 / Biso mean: 59.2954 Å2 / Biso min: 25.4 Å2
Refinement stepCycle: final / Resolution: 2.3→41.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 43 97 3250
Biso mean--89.11 54.11 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083247
X-RAY DIFFRACTIONf_angle_d0.8724389
X-RAY DIFFRACTIONf_chiral_restr0.048487
X-RAY DIFFRACTIONf_plane_restr0.005556
X-RAY DIFFRACTIONf_dihedral_angle_d13.3171968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.39220.26841290.218226482777100
2.3922-2.50110.21521330.201726652798100
2.5011-2.63290.24861320.198726992831100
2.6329-2.79780.31280.204926882816100
2.7978-3.01380.22341450.193327182863100
3.0138-3.3170.21831200.197927592879100
3.317-3.79660.2731460.177527632909100
3.7966-4.78220.20451650.154127852950100
4.7822-41.03150.2231320.18582998313097
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)
10.4208-0.17020.80832.3218-0.3373.1013-0.0297-0.0575-0.2596-0.2461-0.0729-0.21120.3691-0.01050.13810.39840.09670.11670.23610.08880.3797-15.8444-36.770452.9063
20.9222-0.29391.75963.9803-0.74593.1147-0.3402-0.42740.03480.58330.3040.66360.1882-0.5798-0.10950.530.14880.17290.41180.13110.5013-24.2951-40.472868.8766
31.1526-0.61090.01662.8145-0.45683.2166-0.03080.19590.2061-0.14440.00060.0307-0.6615-0.3427-0.00880.47320.160.0990.38460.08640.4095-19.0544-21.53349.064
40.9324-0.3065-0.06051.914-0.54563.6522-0.01490.08550.1667-0.17390.0309-0.0904-0.3932-0.19130.02160.40540.13020.10080.27910.08050.379-17.369-25.624949.2208
51.88570.0305-1.07490.35260.92382.8906-0.2672-0.25080.1898-0.2096-0.16-0.4113-0.1660.93060.1440.5858-0.12630.1080.60960.20090.73544.6562-17.960740.205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 330 )A265 - 330
2X-RAY DIFFRACTION2chain 'A' and (resid 331 through 363 )A331 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 475 )A364 - 475
4X-RAY DIFFRACTION4chain 'A' and (resid 476 through 652 )A476 - 652
5X-RAY DIFFRACTION5chain 'A' and (resid 653 through 713 )A653 - 713

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