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- PDB-7nuh: Influenza A/California/07/2009(H1N1) endonuclease with I38T mutat... -

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Basic information

Entry
Database: PDB / ID: 7nuh
TitleInfluenza A/California/07/2009(H1N1) endonuclease with I38T mutation 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 / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
: / DI(HYDROXYETHYL)ETHER / Orientin / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23911
Polymers21,1961
Non-polymers1,04310
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-1 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.967, 73.967, 127.575
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-322-

HOH

21A-471-

HOH

31A-477-

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: 21196.129 Da / Num. of mol.: 1 / Mutation: I38T
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 , 6 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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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 / Orientin


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting 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: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.2→45.24 Å / Num. obs: 10985 / % possible obs: 99.2 % / Redundancy: 6.793 % / Biso Wilson estimate: 41.708 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.095 / Χ2: 0.891 / Net I/σ(I): 15.96 / Num. measured all: 74623 / Scaling rejects: 17
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
2.2-2.264.1871.1661.2132247857700.3861.32598.1
2.26-2.324.1680.9611.5232437867780.4931.09199
2.32-2.394.1850.9341.6231607587550.5461.06299.6
2.39-2.464.3290.7441.9931607317300.6830.84599.9
2.46-2.544.4640.6452.3931477077050.7580.72899.7
2.54-2.634.5460.483.1830876806790.8620.54199.9
2.63-2.735.6010.4324.1337476786690.8790.47898.7
2.73-2.846.8370.3315.8944586526520.9410.36100
2.84-2.977.430.267.8645996196190.9650.281100
2.97-3.117.8290.17611.7346665965960.9840.189100
3.11-3.288.5760.1411547515655540.9860.1598.1
3.28-3.488.7750.09322.3147125455370.9950.09998.5
3.48-3.7210.0450.06730.4551335125110.9990.07199.8
3.72-4.0210.2620.05339.3249264814800.9990.05699.8
4.02-4.410.3290.04245.9646484514500.9990.04599.8
4.4-4.9210.0120.03948.8641254144120.9990.04299.5
4.92-5.6810.0190.04939.9536573693650.9990.05298.9
5.68-6.969.5850.05240.4729813163110.9990.05598.4
6.96-9.848.8670.02563.69226126325510.02797
9.84-45.245.9750.02359.0693816715710.02594

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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: 2.2→45.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1533 / FOM work R set: 0.7638 / SU B: 9.178 / SU ML: 0.216 / SU R Cruickshank DPI: 0.2974 / SU Rfree: 0.2397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 549 5 %RANDOM
Rwork0.1927 ---
obs0.1963 10437 99.17 %-
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: 115.09 Å2 / Biso mean: 42.106 Å2 / Biso min: 18.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2.2→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 66 192 1687
Biso mean--55.92 54.8 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181386
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6932078
X-RAY DIFFRACTIONr_angle_other_deg1.2761.5923183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91121.62886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1291512
X-RAY DIFFRACTIONr_chiral_restr0.060.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 36 -
Rwork0.314 731 -
all-767 -
obs--97.96 %

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