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- PDB-6euw: Crystal structure of the cap-binding domain of the PB2 subunit of... -

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Basic information

Entry
Database: PDB / ID: 6euw
TitleCrystal structure of the cap-binding domain of the PB2 subunit of influenza A/H5N1 polymerase bound to an azaindazole inhibitor
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / influenza RNA-dependent RNA polymerase / PB2 subunit / cap-binding domain / 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 / 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 A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8334
Polymers18,2481
Non-polymers5853
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-1 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.490, 62.490, 69.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Polymerase basic protein 2


Mass: 18248.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 424-loop deletion variant Replace 421-VNRANQR by GSG
Source: (gene. exp.) Influenza A virus (A/duck/Shantou/4610/2003(H5N1))
Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2LG68
#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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di NaH phosphate and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0615 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0615 Å / Relative weight: 1
ReflectionResolution: 1→54.12 Å / Num. obs: 74557 / % possible obs: 94 % / Redundancy: 4.46 % / CC1/2: 0.996 / Rsym value: 0.065 / Net I/σ(I): 12.61
Reflection shellResolution: 1→1.06 Å / Redundancy: 2.04 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 9463 / CC1/2: 0.846 / Rsym value: 0.508 / % possible all: 70.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CB7

4cb7


Resolution: 1→54.12 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.85 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16376 3907 5 %RANDOM
Rwork0.13945 ---
obs0.14063 74557 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1→54.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 41 151 1418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191416
X-RAY DIFFRACTIONr_bond_other_d0.0020.021351
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9971918
X-RAY DIFFRACTIONr_angle_other_deg1.10133137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71923.27658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6131513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02285
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_it1.5751.614694
X-RAY DIFFRACTIONr_mcbond_other1.5531.611693
X-RAY DIFFRACTIONr_mcangle_it2.1112.429885
X-RAY DIFFRACTIONr_mcangle_other2.112.434886
X-RAY DIFFRACTIONr_scbond_it2.2972.033722
X-RAY DIFFRACTIONr_scbond_other2.2972.032722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7282.9041034
X-RAY DIFFRACTIONr_long_range_B_refined3.28120.2081519
X-RAY DIFFRACTIONr_long_range_B_other3.28320.2271520
X-RAY DIFFRACTIONr_rigid_bond_restr1.67532767
X-RAY DIFFRACTIONr_sphericity_free31.365100
X-RAY DIFFRACTIONr_sphericity_bonded9.50252788
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 204 -
Rwork0.388 3475 -
obs--59.66 %

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