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- PDB-4nce: Influenza polymerase basic protein 2 (PB2) bound to 7-methyl-GTP -

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Basic information

Entry
Database: PDB / ID: 4nce
TitleInfluenza polymerase basic protein 2 (PB2) bound to 7-methyl-GTP
ComponentsPolymerase basic protein 2
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / influenza virus / cap-binding domain / TRANSCRIPTION-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 / virus-mediated perturbation of host defense response / viral RNA genome replication / RNA-dependent RNA polymerase activity / 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 / virus-mediated perturbation of host defense response / viral RNA genome replication / RNA-dependent RNA polymerase activity / 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-11H / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJacobs, M.D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of a Novel, First-in-Class, Orally Bioavailable Azaindole Inhibitor (VX-787) of Influenza PB2.
Authors: Clark, M.P. / Ledeboer, M.W. / Davies, I. / Byrn, R.A. / Jones, S.M. / Perola, E. / Tsai, A. / Jacobs, M. / Nti-Addae, K. / Bandarage, U.K. / Boyd, M.J. / Bethiel, R.S. / Court, J.J. / Deng, ...Authors: Clark, M.P. / Ledeboer, M.W. / Davies, I. / Byrn, R.A. / Jones, S.M. / Perola, E. / Tsai, A. / Jacobs, M. / Nti-Addae, K. / Bandarage, U.K. / Boyd, M.J. / Bethiel, R.S. / Court, J.J. / Deng, H. / Duffy, J.P. / Dorsch, W.A. / Farmer, L.J. / Gao, H. / Gu, W. / Jackson, K. / Jacobs, D.H. / Kennedy, J.M. / Ledford, B. / Liang, J. / Maltais, F. / Murcko, M. / Wang, T. / Wannamaker, M.W. / Bennett, H.B. / Leeman, J.R. / McNeil, C. / Taylor, W.P. / Memmott, C. / Jiang, M. / Rijnbrand, R. / Bral, C. / Germann, U. / Nezami, A. / Zhang, Y. / Salituro, F.G. / Bennani, Y.L. / Charifson, P.S.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)20,4504
Polymers19,1741
Non-polymers1,2763
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 81.440, 54.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / Fragment: CAP-BINDING DOMAIN / Mutation: R389K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: strain A/Victoria/3/1975 H3N2 / Gene: PB2, polymerase basic protein / Plasmid details: with an N-terminal TEV cleavable 6*His tag / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: P31345
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Chemical ChemComp-11H / 9,10-dioxo-9,10-dihydroanthracene-2,6-disulfonic acid


Mass: 368.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8O8S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.7 uL of protein solution (9.7 mg/mL protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 5 mM m7GTP) was mixed with 0.35 uL Hampton Research Silver Bullet ...Details: 0.7 uL of protein solution (9.7 mg/mL protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 5 mM m7GTP) was mixed with 0.35 uL Hampton Research Silver Bullet screening reagent #36. This mixture was combined with 0.35 uL of well solution (approximately 1.3 M sodium formate, 100 mM sodium citrate buffer pH 4.6, 5 mM dithiothreitol) and suspended over 1 mL of well solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Aug 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.62 Å / Num. all: 9272 / Num. obs: 9272 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.45 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQZ

2vqz


Resolution: 2.3→29.62 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.39 / SU ML: 0.167 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22929 442 4.8 %RANDOM
Rwork0.1946 ---
all0.19625 9272 --
obs0.19625 8830 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å2-0 Å2
2--0.85 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 81 43 1414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221421
X-RAY DIFFRACTIONr_angle_refined_deg1.3862.0231930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34923.33363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3651513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021071
X-RAY DIFFRACTIONr_mcbond_it0.4441.5817
X-RAY DIFFRACTIONr_mcangle_it0.89321321
X-RAY DIFFRACTIONr_scbond_it1.5963604
X-RAY DIFFRACTIONr_scangle_it2.624.5607
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 31 -
Rwork0.266 644 -
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)
10.7742-0.06010.2292.27210.41930.8735-0.00370.0366-0.0838-0.0202-0.0280.23570.052-0.14880.03170.05670.00220.01140.03910.00260.019-41.3469-2.01962.0527
21.52760.6595-0.43945.8249-1.43372.2642-0.07130.02970.0922-0.07910.0099-0.3705-0.09750.05170.06140.04080.0074-0.00660.0511-0.03830.0392-32.30941.14095.2695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 416
2X-RAY DIFFRACTION1A502
3X-RAY DIFFRACTION2A417 - 483

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