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- PDB-5buh: Influenza PB2 bound to a hydroxymethyl azaindole inhibitor -

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Basic information

Entry
Database: PDB / ID: 5buh
TitleInfluenza PB2 bound to a hydroxymethyl azaindole inhibitor
ComponentsPolymerase basic protein 2
KeywordsIMMUNE SYSTEM / small molecule inhibitor / polymerase / influenza
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: 2.55 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
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.801, 81.801, 55.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsMonomer confirmed by size exclusion chromatography

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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
Details: N-terminal cloning artifact / 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.: 27 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1 microL protein solution (2.8 mg/ml protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) and 0.4 ...Details: 1 microL protein solution (2.8 mg/ml protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) and 0.4 ?L well solution (1.5 M sodium formate, 100 mM sodium citrate buffer pH 4.7, 10 mM dithiothreitol) was suspended over 1 mL of well solution. The crystals were transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate buffer pH 4.7) containing 1 mM small-molecule inhibitor. Crystals were incubated approximately 15 hours t 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: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→26.78 Å / Num. all: 7617 / Num. obs: 6918 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 66.59 Å2 / Rmerge(I) obs: 0.051 / Net I/av σ(I): 15.7 / Net I/σ(I): 17.1 / Num. measured all: 29301
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all% possible all
2.55-2.854.20.386410197598
8.06-26.784.10.02592122696.9

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Processing

Software
NameVersionClassification
autoPROCdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→26.78 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9502 / SU R Cruickshank DPI: 0.421 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 339 4.9 %RANDOM
Rwork0.1703 ---
obs0.1716 6915 98.67 %-
Displacement parametersBiso max: 179.66 Å2 / Biso mean: 65.57 Å2 / Biso min: 29.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.7385 Å20 Å20 Å2
2--0.7385 Å20 Å2
3----1.4769 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: final / Resolution: 2.55→26.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 61 27 1368
Biso mean--65.83 55.23 -
Num. residues----163
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d507SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes224HARMONIC5
X-RAY DIFFRACTIONt_it1367HARMONIC20
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_contact1507SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1367HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1864HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion20.73
LS refinement shellResolution: 2.55→2.85 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3274 98 5.07 %
Rwork0.1907 1836 -
all0.197 1934 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: -37.8885 Å / Origin y: -0.5611 Å / Origin z: 2.8317 Å
111213212223313233
T0.0054 Å20.0585 Å20.0517 Å2--0.2055 Å20.0279 Å2---0.2161 Å2
L1.4676 °2-0.3177 °20.2095 °2-9.236 °23.9209 °2--3.8796 °2
S-0.0833 Å °0.1187 Å °-0.0245 Å °-0.6418 Å °0.1358 Å °-0.0245 Å °-0.45 Å °0.1979 Å °-0.0524 Å °
Refinement TLS groupSelection details: { A|21 - A|183 }

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