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- PDB-6fs6: Influenza A/California/04/2009 (pH1N1) endonuclease with bound in... -

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Basic information

Entry
Database: PDB / ID: 6fs6
TitleInfluenza A/California/04/2009 (pH1N1) endonuclease 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 / 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
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: 2.291 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

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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)138,71424
Polymers135,1546
Non-polymers3,56018
Water3,549197
1
A: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1194
Polymers22,5261
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)23,1194
Polymers22,5261
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)23,1194
Polymers22,5261
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)23,1194
Polymers22,5261
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)23,1194
Polymers22,5261
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)23,1194
Polymers22,5261
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.180, 75.690, 121.590
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: 22525.717 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: N-terminal GMGSGMA linker residues 52-64 replaced by glycine,N-terminal GMGSGMA linker residues 52-64 replaced by glycine
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.: 197 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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 0.3 M (NH4)2SO4, 0.1 M ADA pH 6.5, 28% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.29→90.401 Å / Num. obs: 59550 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rsym value: 0.083 / Net I/σ(I): 14.8
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4199 / CC1/2: 0.77 / % possible all: 100

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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: 2.291→90.401 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2306 2796 4.93 %
Rwork0.1934 --
obs0.1953 56754 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.291→90.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8796 0 216 197 9209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049346
X-RAY DIFFRACTIONf_angle_d0.84712579
X-RAY DIFFRACTIONf_dihedral_angle_d15.6065649
X-RAY DIFFRACTIONf_chiral_restr0.0461314
X-RAY DIFFRACTIONf_plane_restr0.0041602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2905-2.330.31981470.25642625X-RAY DIFFRACTION100
2.33-2.37240.26621570.23362657X-RAY DIFFRACTION100
2.3724-2.4180.28631400.22652664X-RAY DIFFRACTION100
2.418-2.46740.26051310.21582669X-RAY DIFFRACTION100
2.4674-2.52110.281360.20662685X-RAY DIFFRACTION100
2.5211-2.57970.29121170.21282661X-RAY DIFFRACTION100
2.5797-2.64420.24831400.21582679X-RAY DIFFRACTION100
2.6442-2.71570.26741510.21832683X-RAY DIFFRACTION100
2.7157-2.79560.24571340.20892658X-RAY DIFFRACTION100
2.7956-2.88590.31671500.22722682X-RAY DIFFRACTION100
2.8859-2.9890.26791170.23712713X-RAY DIFFRACTION100
2.989-3.10870.27911500.2222660X-RAY DIFFRACTION100
3.1087-3.25020.27111550.20732675X-RAY DIFFRACTION100
3.2502-3.42160.24271240.20622711X-RAY DIFFRACTION100
3.4216-3.6360.23241370.19312701X-RAY DIFFRACTION100
3.636-3.91670.19761370.17172695X-RAY DIFFRACTION99
3.9167-4.31080.20661440.16142731X-RAY DIFFRACTION100
4.3108-4.93460.18641520.15432733X-RAY DIFFRACTION100
4.9346-6.21690.2151320.19942793X-RAY DIFFRACTION100
6.2169-90.47150.18561450.1852883X-RAY DIFFRACTION99

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