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- PDB-6fs8: Influenza B/Memphis/13/03 endonuclease with bound inhibitor, balo... -

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Basic information

Entry
Database: PDB / ID: 6fs8
TitleInfluenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Influenza / endonuclease / inhibitor
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
Baloxavir acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCusack, S. / Speranzini, V.
CitationJournal: Sci Rep / Year: 2018
Title: Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil.
Authors: Omoto, S. / Speranzini, V. / Hashimoto, T. / Noshi, T. / Yamaguchi, H. / Kawai, M. / Kawaguchi, K. / Uehara, T. / Shishido, T. / Naito, A. / Cusack, S.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Polymerase acidic protein
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2248
Polymers47,0372
Non-polymers1,1876
Water3,171176
1
B: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1124
Polymers23,5191
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1124
Polymers23,5191
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.820, 59.820, 125.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 23518.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal linker GAMGSGMA / Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PA / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H19F2N3O4S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for ...Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M NaCl, 0.1 M Na(CH3)2AsO2 pH 6.5, 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.254 Å / Relative weight: 1
ReflectionResolution: 1.8→59.86 Å / Num. obs: 37506 / % possible obs: 91.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.862 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:5FML

5fml


Resolution: 1.8→59.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.539 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21507 1758 4.7 %RANDOM
Rwork0.18344 ---
obs0.18494 35748 91.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å2-0 Å2
2--0.62 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.8→59.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 72 176 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023162
X-RAY DIFFRACTIONr_bond_other_d0.0020.022903
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9964288
X-RAY DIFFRACTIONr_angle_other_deg0.90736769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1675377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74425.17147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it1.6252.2771490
X-RAY DIFFRACTIONr_mcbond_other1.6172.2751489
X-RAY DIFFRACTIONr_mcangle_it2.5953.3881873
X-RAY DIFFRACTIONr_mcangle_other2.5963.3891874
X-RAY DIFFRACTIONr_scbond_it2.082.5391672
X-RAY DIFFRACTIONr_scbond_other2.0792.5381673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3223.7022416
X-RAY DIFFRACTIONr_long_range_B_refined4.54525.8813677
X-RAY DIFFRACTIONr_long_range_B_other4.50125.7983652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 141 -
Rwork0.26 2651 -
obs--93.66 %

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