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- PDB-6eux: Structure of the midlink and cap-binding domains of influenza B p... -

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Basic information

Entry
Database: PDB / ID: 6eux
TitleStructure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / Influenza B polymerase PB2 subunit cap-binding domain cap-binding inhibitor
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed 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 polymerase PB2 C-terminal 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 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Chem-BYB / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCusack, S. / Gaudon, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.
Authors: Pflug, A. / Gaudon, S. / Resa-Infante, P. / Lethier, M. / Reich, S. / Schulze, W.M. / Cusack, S.
History
DepositionOct 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Author supporting evidence / Database references / Source and taxonomy
Category: citation / entity_src_gen / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4062
Polymers33,0061
Non-polymers4001
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.200, 73.200, 103.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-784-

HOH

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Components

#1: Protein Polymerase basic protein 2


Mass: 33006.055 Da / Num. of mol.: 1 / Fragment: cap-midlink double domain (residues 249-540)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PB2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q5V8X3
#2: Chemical ChemComp-BYB / (2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid


Mass: 400.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18F2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals were obtained by mixing FluB double domain at 15 mg/ml in 50 mM Tris pH 7.5 and 10% glycerol and 5 mM of VX-787 with 0.1 M PTCP and 25% PEG1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20671 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.46
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 5.78 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.75 / CC1/2: 0.644 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSA

4wsa


Resolution: 2.05→40.14 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.742 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25404 1022 4.9 %RANDOM
Rwork0.22945 ---
obs0.23065 19649 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.898 Å2
Baniso -1Baniso -2Baniso -3
1-11.63 Å20 Å20 Å2
2--11.63 Å20 Å2
3----23.26 Å2
Refinement stepCycle: 1 / Resolution: 2.05→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 29 102 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191916
X-RAY DIFFRACTIONr_bond_other_d0.0010.021829
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9852576
X-RAY DIFFRACTIONr_angle_other_deg0.83534235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8823.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9841519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4335.093934
X-RAY DIFFRACTIONr_mcbond_other1.4335.092933
X-RAY DIFFRACTIONr_mcangle_it2.5177.5581171
X-RAY DIFFRACTIONr_mcangle_other2.5167.5591172
X-RAY DIFFRACTIONr_scbond_it1.3515.051982
X-RAY DIFFRACTIONr_scbond_other1.3515.052983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3797.5551406
X-RAY DIFFRACTIONr_long_range_B_refined4.83556.4422085
X-RAY DIFFRACTIONr_long_range_B_other4.71556.3922072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 74 -
Rwork0.327 1421 -
obs--99.47 %

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