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- PDB-8pup: Influenza A/California/07/2009(H1N1) endonuclease in complex with... -

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Basic information

Entry
Database: PDB / ID: 8pup
TitleInfluenza A/California/07/2009(H1N1) endonuclease in complex with purpurogallin-like compound
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase / endonuclease inhibitor / purpurogallin / antivirals
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
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
Similarity search - Domain/homology
: / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKotacka, T. / Radilova, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: Chemmedchem / Year: 2025
Title: 3'-Dehydroxypurpurogallin-4-Carboxamides as Influenza A Endonuclease Inhibitors: Synthesis, Structure-Activity Relationship Analysis, and Structural Characterization of Protein Complex.
Authors: Kral, M. / Kotacka, T. / Reiberger, R. / Panyrkova, G. / Radilova, K. / Osifova, Z. / Flieger, M. / Konvalinka, J. / Majer, P. / Kozisek, M. / Machara, A.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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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)22,3839
Polymers21,6411
Non-polymers7438
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint4 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.950, 73.950, 126.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21640.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 76 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-H2I / ~{N}-[(4-hydroxyphenyl)methyl]-3,4,6-tris(oxidanyl)-5-oxidanylidene-benzo[7]annulene-8-carboxamide


Mass: 353.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15NO6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 28879 / % possible obs: 99 % / Redundancy: 17.2 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.101 / Net I/σ(I): 19.85
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.93-2.052.16744940.2962.3311
2.05-2.191.11543750.741.1671
2.19-2.360.67841080.940.6971
2.36-2.590.43437950.9810.4451
2.59-2.890.23934160.9930.2451
2.89-3.340.12530440.9980.1281
3.34-4.080.058255710.0591
4.08-5.750.039197810.041
5.75-500.03111210.0311

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.02 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.85 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26548 721 5 %RANDOM
Rwork0.21587 ---
obs0.21831 13683 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å20 Å2
3---1.49 Å2
Refinement stepCycle: 1 / Resolution: 2→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 48 68 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121527
X-RAY DIFFRACTIONr_bond_other_d0.0080.0161374
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.6822047
X-RAY DIFFRACTIONr_angle_other_deg0.4431.5753146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.24521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98510252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9954.848727
X-RAY DIFFRACTIONr_mcbond_other3.9884.848727
X-RAY DIFFRACTIONr_mcangle_it5.3978.692907
X-RAY DIFFRACTIONr_mcangle_other5.3948.696908
X-RAY DIFFRACTIONr_scbond_it4.1145.083800
X-RAY DIFFRACTIONr_scbond_other4.1115.081801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0189.2021141
X-RAY DIFFRACTIONr_long_range_B_refined7.88944.91761
X-RAY DIFFRACTIONr_long_range_B_other7.88744.891762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 49 -
Rwork0.308 945 -
obs--96.04 %

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