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- PDB-5f79: Influenza PB2 bound to an azaindole inhibitor -

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Basic information

Entry
Database: PDB / ID: 5f79
TitleInfluenza PB2 bound to an azaindole inhibitor
ComponentsPolymerase basic protein 2
KeywordsTranscription/Inhibitor / small molecule inhibitor / polymerase / Transcription-Inhibitor complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Chem-4V7 / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsJacobs, M.D.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Novel 2-Substituted 7-Azaindole and 7-Azaindazole Analogues as Potential Antiviral Agents for the Treatment of Influenza.
Authors: Bandarage, U.K. / Clark, M.P. / Perola, E. / Gao, H. / Jacobs, M.D. / Tsai, A. / Gillespie, J. / Kennedy, J.M. / Maltais, F. / Ledeboer, M.W. / Davies, I. / Gu, W. / Byrn, R.A. / Nti Addae, ...Authors: Bandarage, U.K. / Clark, M.P. / Perola, E. / Gao, H. / Jacobs, M.D. / Tsai, A. / Gillespie, J. / Kennedy, J.M. / Maltais, F. / Ledeboer, M.W. / Davies, I. / Gu, W. / Byrn, R.A. / Nti Addae, K. / Bennett, H. / Leeman, J.R. / Jones, S.M. / O'Brien, C. / Memmott, C. / Bennani, Y. / Charifson, P.S.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 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 basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6462
Polymers19,1741
Non-polymers4721
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.970, 80.970, 54.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 19174.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Beijing/39/1975 H3N2 / Gene: PB2 / Plasmid: pET28b.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q30NP1
#2: Chemical ChemComp-4V7 / N-[(1R,3S)-3-({5-fluoro-2-[5-fluoro-2-(hydroxymethyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]pyrimidin-4-yl}amino)cyclohexyl]pyrrolidine-1-carboxamide


Mass: 471.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27F2N7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well ...Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.26→43.09 Å / Num. obs: 9658 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 61.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Net I/σ(I): 25.9 / Num. measured all: 47689
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.26-2.4450.5583.2981819720.850.279100
5.98-43.094.80.01372.9260854710.00799.6

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4NCE

4nce


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9496 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.29 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 392 4.86 %RANDOM
Rwork0.1677 ---
obs0.1694 8073 99.94 %-
Displacement parametersBiso max: 218.49 Å2 / Biso mean: 68.14 Å2 / Biso min: 32.59 Å2
Baniso -1Baniso -2Baniso -3
1--4.4024 Å20 Å20 Å2
2---4.4024 Å20 Å2
3---8.8048 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 33 51 1364
Biso mean--104.76 61.45 -
Num. residues----163
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d505SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes219HARMONIC5
X-RAY DIFFRACTIONt_it1339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion174SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1530SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1339HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1799HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion19.45
LS refinement shellResolution: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2697 105 4.63 %
Rwork0.1942 2165 -
all0.1977 2270 -
obs--100 %
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)
1-0.09290.72471.20585.60552.83744.509-0.09230.1010.054-0.668-0.12120.4376-0.3843-0.05830.21350.01760.0874-0.0103-0.1518-0.0052-0.0935-41.8335-1.2781.7131
24.3549-0.69131.902415.4913-1.24397.675-0.097-0.0419-0.2850.26920.2017-1.04610.20060.6101-0.10470.0110.1890.0528-0.2026-0.0992-0.1072-33.2267-5.41845.8395
32.50563.91422.76723.78190.77179.0324-0.07070.54930.1238-1.26780.2435-0.9302-0.85120.4181-0.17280.1772-0.12820.2035-0.181-0.0276-0.0823-29.790312.06320.8966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|21 - 114}A1 - 114
2X-RAY DIFFRACTION2{A|115 - 158}A115 - 158
3X-RAY DIFFRACTION3{A|159 - 183}A159 - 183

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