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- PDB-5wl0: Co-crystal structure of Influenza A H3N2 PB2 (241-741) bound to VX-787 -

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Basic information

Entry
Database: PDB / ID: 5wl0
TitleCo-crystal structure of Influenza A H3N2 PB2 (241-741) bound to VX-787
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN/INHIBITOR / Polymerase basic protein 2 / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


virion component => GO:0044423 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 CAP binding domain
Similarity search - Domain/homology
Chem-21G / DI(HYDROXYETHYL)ETHER / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMa, X. / Shia, S.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for therapeutic inhibition of influenza A polymerase PB2 subunit.
Authors: Ma, X. / Xie, L. / Wartchow, C. / Warne, R. / Xu, Y. / Rivkin, A. / Tully, D. / Shia, S. / Uehara, K. / Baldwin, D.M. / Muiru, G. / Zhong, W. / Zaror, I. / Bussiere, D.E. / Leonard, V.H.J.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0903
Polymers57,5851
Non-polymers5062
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.413, 56.752, 82.014
Angle α, β, γ (deg.)90.000, 111.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-664-

ARG

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Components

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


Mass: 57584.965 Da / Num. of mol.: 1 / Fragment: UNP residues 241-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Udorn/307/1972 H3N2)
Strain: A/Udorn/307/1972 H3N2 / Gene: PB2 / Plasmid: pTrcHis2B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q67296
#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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.86 % / Description: Rods
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.77 / Details: 0.1 M MES, pH 5.77, 13.18% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43 Å / Num. obs: 24138 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 46.67 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.07
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2401 / CC1/2: 0.678 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2JDQ & 2VQZ

2jdq

2vqz


Resolution: 2.4→43 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6
RfactorNum. reflection% reflection
Rfree0.2531 1164 4.88 %
Rwork0.203 --
obs0.2055 23874 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.47 Å2 / Biso mean: 63.2993 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 2.4→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 36 45 3872
Biso mean--55.27 54.56 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013885
X-RAY DIFFRACTIONf_angle_d1.175237
X-RAY DIFFRACTIONf_chiral_restr0.063599
X-RAY DIFFRACTIONf_plane_restr0.007697
X-RAY DIFFRACTIONf_dihedral_angle_d17.8392398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.50930.35041490.294528162965100
2.5093-2.64150.34931510.274628783029100
2.6415-2.8070.33141490.254527922941100
2.807-3.02370.30961290.252328863015100
3.0237-3.32790.33231350.221528783013100
3.3279-3.80920.25341380.19232855299399
3.8092-4.79810.20731510.16722796294797
4.7981-43.00670.20191620.17712809297196
Refinement TLS params.Method: refined / Origin x: -16.2107 Å / Origin y: 27.8718 Å / Origin z: 16.5666 Å
111213212223313233
T0.1744 Å2-0.0237 Å2-0.0272 Å2-0.1694 Å20.0636 Å2--0.1899 Å2
L0.5065 °20.752 °20.3644 °2-0.4418 °20.6532 °2--0.7216 °2
S0.1086 Å °0.0242 Å °-0.0632 Å °0.0606 Å °-0.1168 Å °0.0183 Å °0.0418 Å °0.0846 Å °0 Å °
Refinement TLS groupSelection details: all

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