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- PDB-6fs7: Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mut... -

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Basic information

Entry
Database: PDB / ID: 6fs7
TitleInfluenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)
ComponentsPolymerase acidic protein,Polymerase 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 / viral translational frameshifting / viral RNA genome replication / symbiont-mediated suppression of host gene expression / 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 / viral translational frameshifting / viral RNA genome replication / symbiont-mediated suppression of host gene expression / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Baloxavir acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein,Polymerase acidic protein
B: Polymerase acidic protein,Polymerase acidic protein
C: Polymerase acidic protein,Polymerase acidic protein
D: Polymerase acidic protein,Polymerase acidic protein
E: Polymerase acidic protein,Polymerase acidic protein
F: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,64224
Polymers135,0826
Non-polymers3,56018
Water9,062503
1
A: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1074
Polymers22,5141
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.680, 75.560, 121.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22513.664 Da / Num. of mol.: 6 / Mutation: I38T,I38T
Source method: isolated from a genetically manipulated source
Details: N-terminal GMGSGMA linkerresidues 52-64 replaced by GlycineI38T mutation,N-terminal GMGSGMA linkerresidues 52-64 replaced by GlycineI38T mutation
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: PA / Plasmid: pESPRIT002 / Production host: Escherichia coli (E. coli)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H19F2N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
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 (NH4)2SO4, 0.1 M Na(CH3)2AsO2 pH 6.5, 30% (w/v) PEG8000

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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: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.96→90.637 Å / Num. obs: 94254 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.994 / Rsym value: 0.043 / Net I/σ(I): 17.4
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 4 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6540 / CC1/2: 0.767 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:4AWK

4awk


Resolution: 1.96→90.637 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.2114 4372 4.86 %
Rwork0.1879 --
obs0.189 89882 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→90.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8945 0 216 503 9664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049375
X-RAY DIFFRACTIONf_angle_d0.79912621
X-RAY DIFFRACTIONf_dihedral_angle_d16.6065662
X-RAY DIFFRACTIONf_chiral_restr0.0491318
X-RAY DIFFRACTIONf_plane_restr0.0041608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9605-1.98270.32111330.25512794X-RAY DIFFRACTION99
1.9827-2.00610.2511660.2612843X-RAY DIFFRACTION100
2.0061-2.03050.2981490.24582800X-RAY DIFFRACTION100
2.0305-2.05620.26541490.22462823X-RAY DIFFRACTION100
2.0562-2.08330.27711560.21952789X-RAY DIFFRACTION100
2.0833-2.11180.24811500.21082856X-RAY DIFFRACTION100
2.1118-2.1420.2481490.21092813X-RAY DIFFRACTION100
2.142-2.1740.24271470.19982843X-RAY DIFFRACTION100
2.174-2.20790.24771480.19892816X-RAY DIFFRACTION100
2.2079-2.24420.23031440.20212832X-RAY DIFFRACTION100
2.2442-2.28290.24681290.19472866X-RAY DIFFRACTION100
2.2829-2.32440.23081290.20132838X-RAY DIFFRACTION100
2.3244-2.36910.24061580.20452843X-RAY DIFFRACTION100
2.3691-2.41740.24011490.20312825X-RAY DIFFRACTION100
2.4174-2.470.27051490.20652847X-RAY DIFFRACTION100
2.47-2.52750.24181490.20072849X-RAY DIFFRACTION100
2.5275-2.59070.2351410.22836X-RAY DIFFRACTION100
2.5907-2.66070.23451390.19562860X-RAY DIFFRACTION100
2.6607-2.7390.22591510.20412835X-RAY DIFFRACTION100
2.739-2.82740.22381450.19672863X-RAY DIFFRACTION99
2.8274-2.92850.23151400.19662831X-RAY DIFFRACTION99
2.9285-3.04580.21891460.19942863X-RAY DIFFRACTION99
3.0458-3.18440.211320.19632872X-RAY DIFFRACTION99
3.1844-3.35230.21631250.19452857X-RAY DIFFRACTION100
3.3523-3.56230.18411390.17742884X-RAY DIFFRACTION99
3.5623-3.83740.19791600.16632836X-RAY DIFFRACTION99
3.8374-4.22350.16631390.15582905X-RAY DIFFRACTION99
4.2235-4.83470.17011470.15032854X-RAY DIFFRACTION98
4.8347-6.0910.20661530.19062911X-RAY DIFFRACTION99
6.091-90.73380.19211610.19213026X-RAY DIFFRACTION98

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