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

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Basic information

Entry
Database: PDB / ID: 4zhz
TitleEndonuclease inhibitor bound to influenza strain H1N1 polymerase acidic subunit N-terminal region with expelling one of 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
5-(2-chlorobenzyl)-2-hydroxy-3-nitrobenzaldehyde / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,0355
Polymers22,3001
Non-polymers7344
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-20 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.562, 66.562, 129.173
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-4P8 / 5-(2-chlorobenzyl)-2-hydroxy-3-nitrobenzaldehyde


Mass: 291.687 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10ClNO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
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 and 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: 2.5→50 Å / Num. obs: 10200 / % possible obs: 95.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 57.82 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.041 / Rrim(I) all: 0.14 / Χ2: 1.03 / Net I/av σ(I): 16.255 / Net I/σ(I): 9.2 / Num. measured all: 126278
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.5412.84860.7860.3151.02393.3
2.54-2.59134910.8690.2750.99995.20.988
2.59-2.6412.74870.830.2341.04894.90.8350.868
2.64-2.69134780.8440.2221.04991.60.7890.821
2.69-2.7512.64970.9040.1861.03994.80.6630.689
2.75-2.8212.84750.9050.1661.04594.20.590.614
2.82-2.8912.74790.9260.1551.04691.90.5480.57
2.89-2.9612.64940.970.1171.04894.50.4110.428
2.96-3.0512.54860.9740.091.01592.20.3180.331
3.05-3.1512.34870.9760.0861.04693.50.3040.316
3.15-3.2612.44910.980.0731.03194.60.2580.268
3.26-3.3912.15120.9820.0571.04895.30.1990.207
3.39-3.5511.95010.9910.0491.00996.30.1730.18
3.55-3.7311.95220.9920.0431.012970.1510.157
3.73-3.9712.25110.9930.0381.0196.60.1310.136
3.97-4.2712.15350.9940.0350.98998.90.1190.125
4.27-4.712.15410.9890.034198.50.1130.118
4.7-5.3812.55440.9920.0291.01999.30.10.105
5.38-6.7812.35680.9940.0271.0551000.090.094
6.78-5011.56150.9930.0271.05997.90.0870.092

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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: 2.5→38.038 Å / FOM work R set: 0.7746 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 472 4.65 %
Rwork0.2222 9681 -
obs0.2243 10153 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.56 Å2 / Biso mean: 41.69 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 2.5→38.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 46 73 1612
Biso mean--70.79 43.86 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041569
X-RAY DIFFRACTIONf_angle_d0.7942108
X-RAY DIFFRACTIONf_chiral_restr0.064218
X-RAY DIFFRACTIONf_plane_restr0.002268
X-RAY DIFFRACTIONf_dihedral_angle_d13.925589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.86180.31341560.25493073322994
2.8618-3.60510.30481600.24123126328694
3.6051-38.04220.24561560.20953482363898

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