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- PDB-7as0: Influenza A PB2 in complex with VX-787 -

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Basic information

Entry
Database: PDB / ID: 7as0
TitleInfluenza A PB2 in complex with VX-787
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / Influenza A / polymerase / cap-snatching / PB2 / VX787
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Chem-21G / BROMIDE ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRadilova, K. / Brynda, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Molecules / Year: 2021
Title: Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase.
Authors: Gregor, J. / Radilova, K. / Brynda, J. / Fanfrlik, J. / Konvalinka, J. / Kozisek, M.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _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 basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1244
Polymers18,5651
Non-polymers5593
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.300, 36.950, 38.340
Angle α, β, γ (deg.)71.120, 75.620, 76.260
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 18564.535 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: PB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3W5X5
#2: Chemical ChemComp-21G / (2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid / 3-[[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid / VX787 / (2S,3S)-3-((5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl)amino)bicyclo[2.2.2]octane-2-carboxylic acid


Mass: 399.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium fluoride, Sodium bromide, Sodium iodide, Imidazole, MES monohydrate (acid), PEG 500, PEG 20000

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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: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.55→35.64 Å / Num. obs: 20014 / % possible obs: 94.7 % / Redundancy: 2.639 % / Biso Wilson estimate: 17.919 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.064 / Χ2: 0.921 / Net I/σ(I): 12.02 / Num. measured all: 52818 / Scaling rejects: 850
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
1.55-1.591.830.1364.272692154414710.9680.18495.3
1.59-1.631.8730.1184.62769153714780.9590.15796.2
1.63-1.681.9770.0845.132930149414820.9830.11199.2
1.68-1.731.980.0855.872796143614120.9810.11398.3
1.73-1.792.010.0786.552723136413550.9840.10399.3
1.79-1.851.9550.0767.222589136713240.9860.10196.9
1.85-1.921.6920.1048.441885130911140.9490.14185.1
1.92-21.7810.0858.76163512399180.9810.11174.1
2-2.092.3020.06311.62574122811180.9870.0891
2.09-2.192.9580.06113.933328113111250.9920.07599.5
2.19-2.311.7860.07713.97167010849350.9760.186.3
2.31-2.453.330.06315.473443105310340.9920.07698.2
2.45-2.623.4540.06617.5631789559200.9810.07996.3
2.62-2.834.2010.05920.1237438988910.9960.06899.2
2.83-3.14.5620.05322.0537778368280.9960.0699
3.1-3.474.2080.05423.4231357577450.9970.06198.4
3.47-44.4680.04826.3829046536500.9960.05499.5
4-4.94.4810.04326.7824875695550.9980.04897.5
4.9-6.933.8140.04623.6516214284250.9960.05399.3
6.93-35.644.0130.04525.959392412340.9970.05297.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P1U

4p1u


Resolution: 1.55→35.64 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1802 / FOM work R set: 0.8296 / SU B: 1.92 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1009 / SU Rfree: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 996 5 %RANDOM
Rwork0.1831 ---
obs0.1849 19032 94.97 %-
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: 54.48 Å2 / Biso mean: 13.779 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å2-0.1 Å2-0.39 Å2
2---0.51 Å20.11 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.55→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 31 205 1484
Biso mean--14.78 26.33 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171281
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6721833
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5922956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01320.41772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0771514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 72 -
Rwork0.261 1394 -
all-1466 -
obs--95.07 %

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