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- PDB-7nug: Influenza A/California/07/2009(H1N1) endonuclease in complex with... -

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Basic information

Entry
Database: PDB / ID: 7nug
TitleInfluenza A/California/07/2009(H1N1) endonuclease in complex with orientin
ComponentsPolymerase acidic protein,Polymerase acidic protein
KeywordsVIRAL PROTEIN / endonuclease / protein-ligand complex / RNA polymerase / Flavonoids
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
Chem-1PG / : / DI(HYDROXYETHYL)ETHER / Orientin / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRadilova, K. / Brynda, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LM2015064 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Int J Mol Sci / Year: 2021
Title: Synthesis and In Vitro Evaluation of C-7 and C-8 Luteolin Derivatives as Influenza Endonuclease Inhibitors.
Authors: Reiberger, R. / Radilova, K. / Kral, M. / Zima, V. / Majer, P. / Brynda, J. / Dracinsky, M. / Konvalinka, J. / Kozisek, M. / Machara, A.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,74213
Polymers21,2081
Non-polymers1,53412
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint14 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.361, 74.361, 126.462
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-345-

HOH

31A-485-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21208.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Strain: 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 , 8 types, 202 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#8: Chemical ChemComp-USE / Orientin / 2-[3,4-bis(oxidanyl)phenyl]-8-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one / 5281675 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-8-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one


Mass: 448.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O11 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.17 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→42.15 Å / Num. obs: 16879 / % possible obs: 99.5 % / Redundancy: 9.31 % / Biso Wilson estimate: 29.266 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.094 / Χ2: 0.907 / Net I/σ(I): 15.29 / Num. measured all: 157145 / Scaling rejects: 109
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.956.1921.1921.67498121912110.5821.30999.3
1.95-26.6950.961.817887117811780.7051.042100
2-2.066.8210.7812.367844115311500.7940.84799.7
2.06-2.127.0180.6033.318029114611440.8660.65299.8
2.12-2.197.4980.4494.098203109410940.9290.483100
2.19-2.277.0930.4674.927448105710500.8980.50599.3
2.27-2.367.3730.3745.227491101710160.9540.40299.9
2.36-2.457.6830.2926.3975989899890.9710.313100
2.45-2.567.8230.2597.4975889709700.9730.277100
2.56-2.697.9060.2069.4572109129120.9850.221100
2.69-2.838.0660.18210.770178708700.9880.194100
2.83-37.1760.13813.5758348318130.9870.14997.8
3-3.218.7160.09219.9266247907600.9960.09896.2
3.21-3.4712.9350.07731.3494817337330.9980.08100
3.47-3.814.2920.05839.6197476826820.9990.06100
3.8-4.2517.4470.04852.8109226286260.9990.0599.7
4.25-4.9119.3630.0457.21092156556410.04299.8
4.91-6.0118.9340.05148.13914548348310.052100
6.01-8.517.8930.04355.4470503943940.9990.045100
8.5-42.1515.0330.03360.59360825024010.03496

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YA5

6ya5


Resolution: 1.9→42.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1701 / FOM work R set: 0.8082 / SU B: 4.517 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1731 / SU Rfree: 0.1628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 845 5 %RANDOM
Rwork0.1951 ---
obs0.1978 16040 99.55 %-
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 max: 91.27 Å2 / Biso mean: 26.456 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å2-0 Å2
2---0.54 Å20 Å2
3---1.75 Å2
Refinement stepCycle: final / Resolution: 1.9→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 101 190 1738
Biso mean--34.28 39.43 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181514
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.692188
X-RAY DIFFRACTIONr_angle_other_deg1.3021.593486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19421.18393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6931514
X-RAY DIFFRACTIONr_chiral_restr0.070.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 61 -
Rwork0.392 1150 -
all-1211 -
obs--99.43 %

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