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- PDB-3l4q: Structural insights into phosphoinositide 3-kinase activation by ... -

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Basic information

Entry
Database: PDB / ID: 3l4q
TitleStructural insights into phosphoinositide 3-kinase activation by the influenza A virus NS1 protein
Components
  • Non-structural protein 1
  • Phosphatidylinositol 3-kinase regulatory subunit beta
KeywordsVIRAL PROTEIN/PROTEIN BINDING / PI3K / PHOSPHOINOSITIDE-3-KINASE / INFLUENZA VIRUS / NS1 / Kinase / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


: / : / Inhibition of IFN-beta / : / Interleukin-7 signaling / Inhibition of PKR / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction ...: / : / Inhibition of IFN-beta / : / Interleukin-7 signaling / Inhibition of PKR / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / Interleukin receptor SHC signaling / PI3K Cascade / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / Inhibition of Host mRNA Processing and RNA Silencing / DAP12 signaling / symbiont-mediated suppression of host mRNA processing / Regulation of signaling by CBL / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / NS1 Mediated Effects on Host Pathways / protein serine/threonine kinase inhibitor activity / regulation of stress fiber assembly / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / G alpha (q) signalling events / RIPK1-mediated regulated necrosis / intracellular glucose homeostasis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / phosphatidylinositol phosphate biosynthetic process / transcription factor binding / Viral mRNA Translation / positive regulation of cell adhesion / regulation of protein localization to plasma membrane / response to endoplasmic reticulum stress / regulation of autophagy / PKR-mediated signaling / ISG15 antiviral mechanism / positive regulation of protein import into nucleus / cellular response to insulin stimulus / protein transport / insulin receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / focal adhesion / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding / nucleus
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Influenza virus non-structural protein, effector domain / Helix Hairpins - #1490 / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Influenza virus non-structural protein, effector domain / Helix Hairpins - #1490 / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / Phosphatidylinositol 3-kinase regulatory subunit beta
Similarity search - Component
Biological speciesInfluenza A virus
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHale, B.G. / Kerry, P.S. / Jackson, D. / Precious, B.L. / Gray, A. / Killip, M.J. / Randall, R.E. / Russell, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural insights into phosphoinositide 3-kinase activation by the influenza A virus NS1 protein
Authors: Hale, B.G. / Kerry, P.S. / Jackson, D. / Precious, B.L. / Gray, A. / Killip, M.J. / Randall, R.E. / Russell, R.J.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
C: Phosphatidylinositol 3-kinase regulatory subunit beta
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3636
Polymers78,1794
Non-polymers1842
Water5,062281
1
A: Non-structural protein 1
C: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,0892
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area17990 Å2
MethodPISA
2
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,0892
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-8 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.950, 98.670, 149.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 18464.219 Da / Num. of mol.: 2 / Fragment: UNP residues 73-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NS / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P03496
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit beta / P85BETA / PI3-kinase p85 subunit beta / PtdIns-3-kinase p85-beta


Mass: 20625.188 Da / Num. of mol.: 2 / Fragment: ISH2 domain, UNP residues 424-593 / Mutation: C495S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PIK3R2 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P23726
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.14 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→82.32 Å / Num. all: 38766 / Num. obs: 36826 / % possible obs: 99.35 %
Reflection shellResolution: 2.3→2.36 Å / % possible all: 98.23

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Processing

SoftwareName: REFMAC / Version: 5.5.0070 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GX9 (chain A, B) and 2V1Y (chain C, D)

2gx9

2v1y


Resolution: 2.3→49.97 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.22 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29232 1940 5 %RANDOM
Rwork0.23195 ---
all0.23499 38766 --
obs0.23499 36826 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.188 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---0.22 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 12 281 4923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.976298
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28324.426244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8215949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271546
X-RAY DIFFRACTIONr_chiral_restr0.1230.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023488
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2761.52811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38524538
X-RAY DIFFRACTIONr_scbond_it3.32331881
X-RAY DIFFRACTIONr_scangle_it5.5494.51760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 137 -
Rwork0.305 2639 -
obs--98.23 %

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