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- PDB-7as2: Influenza A PB2 (M431 mutation) in complex with VX-787 -

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Basic information

Entry
Database: PDB / ID: 7as2
TitleInfluenza A PB2 (M431 mutation) in complex with VX-787
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / Influenza A / polymerase / Polymerase basic protein 2 / 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-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 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Chem-21G / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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)18,9462
Polymers18,5461
Non-polymers3991
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.190, 37.120, 38.450
Angle α, β, γ (deg.)71.850, 75.390, 75.920
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: 18546.498 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Magnesium chloride, Calcium chloride, Tris (base), BICINE, 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: Aug 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.72→24.34 Å / Num. obs: 11714 / % possible obs: 75.3 % / Redundancy: 1.847 % / Biso Wilson estimate: 24.548 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.05 / Χ2: 0.94 / Net I/σ(I): 14.81 / Num. measured all: 21632
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
1.72-1.821.4870.1992.999625106700.8920.28126.7
1.82-1.951.8340.144.963197237017430.9470.19773.5
1.95-2.11.9520.0759.123535219518110.9870.10682.5
2.1-2.31.9410.05612.323466200417860.9910.0889.1
2.3-2.581.9090.04514.713142184416460.9950.06389.3
2.58-2.971.8730.03418.492707162214450.9960.04889.1
2.97-3.631.7230.02424.62033136111800.9980.03586.7
3.63-5.111.6580.01929.78146610568840.9980.02783.7
5.11-24.341.9850.0223310905985490.9970.03291.8

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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: 1.75→24.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1994 / WRfactor Rwork: 0.1589 / FOM work R set: 0.8741 / SU B: 2.48 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1544 / SU Rfree: 0.1385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 610 5 %RANDOM
Rwork0.1597 ---
obs0.162 11584 82.79 %-
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: 47.47 Å2 / Biso mean: 17.289 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0.1 Å2-0.24 Å2
2--0.36 Å2-0.43 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.75→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 29 170 1450
Biso mean--17.17 26.15 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131335
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171264
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6761806
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5962925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79420.59767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0281512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 14 -
Rwork0.236 274 -
all-288 -
obs--26.62 %

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