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

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Basic information

Entry
Database: PDB / ID: 5ifb
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to follow on fragment EBSI-4719 5-chloro-2-(1H-imidazol-1-yl)aniline
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 / 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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
5-chloro-2-(1H-imidazol-1-yl)aniline / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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)53,4044
Polymers53,0971
Non-polymers3073
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area19170 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8088
Polymers106,1932
Non-polymers6146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3640 Å2
ΔGint-29 kcal/mol
Surface area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.920, 68.920, 396.420
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-6AV / 5-chloro-2-(1H-imidazol-1-yl)aniline


Mass: 193.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8ClN3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mg/mL protein against Morpheus screen condition E10 with 10% PEG 8000, 20% EG, 0.03 M each ethylene glycol, 0.1 M Trizma/bicine pH 8.5, crystal tracking ID 256486e10, unique puck ID lum0-1

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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: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.45→47.685 Å / Num. obs: 21735 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 37.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.45-2.510.5153.031100
2.51-2.580.4773.31199.9
2.58-2.660.4253.61199.9
2.66-2.740.3434.521100
2.74-2.830.2855.58199.7
2.83-2.930.2177.11199.9
2.93-3.040.1798.371100
3.04-3.160.13110.951100
3.16-3.30.11512.68199.8
3.3-3.460.08416.78199.7
3.46-3.650.06620.411100
3.65-3.870.05722.77199.7
3.87-4.140.0526.42199.8
4.14-4.470.04328.62199.6
4.47-4.90.0430.95199.8
4.9-5.480.0429.45198.8
5.48-6.330.04326.32198.8
6.33-7.750.03829.09198.4
7.75-10.960.02735.72197.9
10.96-47.6850.02534.48192.5

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Processing

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

4iuj


Resolution: 2.45→47.685 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.2309 1074 4.94 %
Rwork0.1752 --
obs0.1781 21734 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.52 Å2 / Biso mean: 45.4789 Å2 / Biso min: 15.91 Å2
Refinement stepCycle: final / Resolution: 2.45→47.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 18 131 3248
Biso mean--67.97 45.06 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073202
X-RAY DIFFRACTIONf_angle_d0.9464343
X-RAY DIFFRACTIONf_chiral_restr0.047491
X-RAY DIFFRACTIONf_plane_restr0.005552
X-RAY DIFFRACTIONf_dihedral_angle_d12.4541937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.56150.2911180.211525182636100
2.5615-2.69660.25151330.209924912624100
2.6966-2.86550.27791180.193525542672100
2.8655-3.08670.25381170.196225312648100
3.0867-3.39730.27761370.177525592696100
3.3973-3.88870.22261450.155625772722100
3.8887-4.89850.18611500.143626262776100
4.8985-47.69360.22051560.18672804296098
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)
10.3063-0.38260.38010.988-0.06511.0666-0.06930.2379-0.185-0.1142-0.019-0.07380.2182-0.198-0.01380.30640.09830.09030.22020.10010.2749-17.0057-36.716353.2108
20.35290.0660.02420.11510.03930.4541-0.14380.1283-0.07710.30560.14430.00170.0911-0.2348-0.02930.36670.15810.08580.27730.08680.2816-24.3957-40.177569.107
30.2506-0.04220.48460.1745-0.22151.1259-0.28130.1772-0.08390.0986-0.1484-0.39640.04050.3789-0.04090.33510.19090.10760.29250.09960.3534-7.059-33.487352.4544
40.399-0.02460.15671.1056-0.51531.5945-0.00710.03010.0526-0.0230.0488-0.0646-0.206-0.19240.00720.24060.14930.07340.1930.05290.2069-20.1029-24.800751.75
50.12080.1442-0.02360.255-0.14180.11960.10890.35560.0832-0.3495-0.0138-0.2422-0.18910.01820.06380.54370.15060.11110.30230.1470.2569-16.0564-13.699534.7066
60.24690.1585-0.09060.21280.01270.0553-0.2926-0.22990.0685-0.0884-0.1428-0.6399-0.26240.5785-0.0150.3891-0.08510.06890.43840.21930.51024.3458-17.759240.0309
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 415 )A364 - 415
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 602 )A416 - 602
5X-RAY DIFFRACTION5chain 'A' and (resid 603 through 652 )A603 - 652
6X-RAY DIFFRACTION6chain 'A' and (resid 653 through 713 )A653 - 713

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