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- PDB-5fdg: Endonuclease inhibitor 3 bound to influenza strain H1N1 polymeras... -

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Basic information

Entry
Database: PDB / ID: 5fdg
TitleEndonuclease inhibitor 3 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-0N8 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 Science 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
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 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_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)22,9205
Polymers22,3001
Non-polymers6204
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.438, 66.438, 126.977
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 / 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-0N8 / (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 413.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClNO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100mM MES, 1.1M ammonium sulfate, 0.1M potassium chloride and 9% trehalose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17513 / % possible obs: 99.2 % / Redundancy: 12 % / Biso Wilson estimate: 37.42 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.035 / Rrim(I) all: 0.12 / Χ2: 1.008 / Net I/av σ(I): 22.15 / Net I/σ(I): 9.6 / Num. measured all: 210260
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1411.31.18280.8040.3391.1521.00498.7
2.14-2.18120.9028470.8550.2670.9411.01498.8
2.18-2.2211.80.7158530.8860.2140.7471.01398.8
2.22-2.2612.40.6378570.9250.1860.6651.01399
2.26-2.31130.6328620.9490.1790.6571.01299
2.31-2.37130.5778490.9550.1640.60.9798.8
2.37-2.4212.80.4888440.9630.140.5091.02198.9
2.42-2.4912.60.4068780.970.1180.4231.02699.3
2.49-2.5611.80.3428470.9760.1030.3580.99698.7
2.56-2.6512.50.38660.9780.0880.3131.03399.3
2.65-2.74120.2768530.9790.0820.2881.03299.2
2.74-2.8512.80.2198750.9860.0630.2280.98699.3
2.85-2.9812.80.1798680.990.0520.1870.99598.5
2.98-3.1412.40.1448760.9930.0420.1511.00299.3
3.14-3.3311.60.1178770.9950.0360.1230.98999.5
3.33-3.5911.60.0938850.9970.0290.0971.02499.7
3.59-3.9511.80.0769060.9980.0240.081.00199.5
3.95-4.5211.40.0649000.9980.020.0671.01899.6
4.52-5.710.60.0589250.9980.0180.0611.014100
5.7-5010.40.05810170.9980.0180.0611.00499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.424

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PHENIXphenix.refine: 1.8.1_116refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQQ

4zqq


Resolution: 2.1→37.764 Å / FOM work R set: 0.8298 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 913 5.23 %
Rwork0.1898 16552 -
obs0.1918 17465 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.52 Å2 / Biso mean: 37.35 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2.1→37.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 36 99 1628
Biso mean--48.36 42.82 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081558
X-RAY DIFFRACTIONf_angle_d1.712093
X-RAY DIFFRACTIONf_chiral_restr0.083219
X-RAY DIFFRACTIONf_plane_restr0.004265
X-RAY DIFFRACTIONf_dihedral_angle_d14.351595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.19710.32191180.22762294241299
2.1971-2.33480.22141460.2072285243199
2.3348-2.5150.27551230.20532334245799
2.515-2.7680.29431270.19542347247499
2.768-3.16840.22331340.19372346248099
3.1684-3.99110.20961160.17724172533100
3.9911-37.77040.20771490.18492529267899

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