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- PDB-5i13: Endonuclease inhibitor 2 bound to influenza strain H1N1 polymeras... -

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Basic information

Entry
Database: PDB / ID: 5i13
TitleEndonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Viral mRNA Translation / 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 / extracellular region / 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
Chem-4P9 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.151 Å
Model detailsRNA binding protein
AuthorsFudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science24590548 Japan
CitationJournal: Biochemistry / Year: 2016
Title: Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit
Authors: Fudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Hoshino, T.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 17, 2016ID: 5FDE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0646
Polymers22,3001
Non-polymers7635
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.580, 66.580, 128.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22300.494 Da / Num. of mol.: 1 / Fragment: endonuclease, residues 1-50, 73-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PA / Plasmid: pET50b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P03433
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-4P9 / 4-{(E)-[2-(4-chlorophenyl)hydrazinylidene]methyl}benzene-1,2,3-triol


Mass: 278.691 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11ClN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Crystals were grown with the reservoir containing 100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride and 9 % trehalose at pH 5.8. Crystal was then soaked with the ligand solution at pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 16066 / % possible obs: 98 % / Redundancy: 9 % / Rmerge(I) obs: 0.074 / Net I/av σ(I): 25.351 / Net I/σ(I): 12.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 9 % / Rmerge(I) obs: 1.034 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation44.2 Å2.52 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREP11.0.05phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQQ

4zqq


Resolution: 2.151→37.956 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09
RfactorNum. reflection% reflection
Rfree0.2328 813 5.07 %
Rwork0.2064 --
obs0.2078 16050 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.18 Å2 / Biso mean: 44.33 Å2 / Biso min: 20.65 Å2
Refinement stepCycle: final / Resolution: 2.151→37.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 45 30 1568
Biso mean--72.67 39.65 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081567
X-RAY DIFFRACTIONf_angle_d0.9852104
X-RAY DIFFRACTIONf_chiral_restr0.067218
X-RAY DIFFRACTIONf_plane_restr0.004268
X-RAY DIFFRACTIONf_dihedral_angle_d15.052589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1514-2.28620.26861380.25952493263199
2.2862-2.46270.3141390.24772501264099
2.4627-2.71050.30561180.23272523264199
2.7105-3.10250.2751510.23122510266198
3.1025-3.90820.22181350.20332553268897
3.9082-37.96210.19561320.1842657278996

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