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- PDB-4zi0: Endonuclease inhibitor bound to influenza strain H1N1 polymerase ... -

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Basic information

Entry
Database: PDB / ID: 4zi0
TitleEndonuclease inhibitor bound to influenza strain H1N1 polymerase acidic subunit N-terminal region without a chelation to the metal ions in the active site
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 / Resolution: 1.802 Å
Model detailsRNA binding protein
AuthorsFudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Neya, S. / 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
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: 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 / diffrn_radiation_wavelength / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7855
Polymers22,3001
Non-polymers4854
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.758, 66.758, 126.744
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-4P9 / 4-{(E)-[2-(4-chlorophenyl)hydrazinylidene]methyl}benzene-1,2,3-triol


Mass: 278.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11ClN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride, 9 % trehalose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27032 / % possible obs: 98.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 37.59 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Χ2: 1.031 / Net I/av σ(I): 36.194 / Net I/σ(I): 16.8 / Num. measured all: 374092
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.8-1.8314.213330.820.3281.015100
1.83-1.8614.113410.8440.2481.0131000.9110.944
1.86-1.914.213360.8940.2231.061000.8180.848
1.9-1.9414.113410.9250.1781.081000.6480.672
1.94-1.9814.213210.9640.1271.0431000.4640.481
1.98-2.0314.313490.9750.0961.0121000.3540.367
2.03-2.0813.913440.9830.0811.0411000.2930.304
2.08-2.1314.313430.9910.0581.0091000.2140.222
2.13-2.214.313500.9930.0420.9851000.1560.162
2.2-2.2714.113410.9950.0381.0661000.1380.143
2.27-2.3514.213500.9960.0320.9741000.1190.123
2.35-2.4414.213590.9970.0281.021000.1020.106
2.44-2.5514.113620.9980.0231.0451000.0850.088
2.55-2.691413510.9980.0210.99699.90.0770.08
2.69-2.861413700.9980.0181.0251000.0670.069
2.86-3.0813.913710.9990.0171.08699.90.0630.065
3.08-3.3913.713860.9980.0170.97399.80.0610.063
3.39-3.8813.113740.9990.0161.07997.90.0530.056
3.88-4.881213330.9990.0121.04893.50.0390.04
4.88-501213770.9990.011.05488.70.0350.037

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREP11.0.05phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M5Q

4m5q


Resolution: 1.802→32.278 Å / FOM work R set: 0.8247 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1354 5.02 %
Rwork0.1998 25612 -
obs0.2011 26966 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.38 Å2 / Biso mean: 44.67 Å2 / Biso min: 24.06 Å2
Refinement stepCycle: final / Resolution: 1.802→32.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 26 203 1722
Biso mean--56.51 55.15 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131547
X-RAY DIFFRACTIONf_angle_d1.4352077
X-RAY DIFFRACTIONf_chiral_restr0.096218
X-RAY DIFFRACTIONf_plane_restr0.006265
X-RAY DIFFRACTIONf_dihedral_angle_d15.157585
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8016-1.86590.2951280.28212530265899
1.8659-1.94060.31511220.272125512673100
1.9406-2.0290.25961470.257525212668100
2.029-2.13590.28291220.237425642686100
2.1359-2.26970.27821410.221125432684100
2.2697-2.44490.24821370.226325722709100
2.4449-2.69080.24091410.212225672708100
2.6908-3.07990.24171480.200825912739100
3.0799-3.87930.20451340.17652616275099
3.8793-32.28360.19181340.18362557269191

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