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- PDB-6ox7: The complex of 1918 NS1-ED and the iSH2 domain of the human p85be... -

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Basic information

Entry
Database: PDB / ID: 6ox7
TitleThe complex of 1918 NS1-ED and the iSH2 domain of the human p85beta subunit of PI3K
Components
  • Non-structural protein 1
  • Phosphatidylinositol 3-kinase regulatory subunit beta
KeywordsVIRAL PROTEIN / NS1 / p85-beta / PI3K / 1918
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / IRS-mediated signalling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / protein serine/threonine kinase inhibitor activity / Signaling by LTK in cancer / Signaling by LTK / PI3K/AKT activation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Signaling by ALK / RHOB GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / CDC42 GTPase cycle / RET signaling / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / negative regulation of MAPK cascade / regulation of protein localization to plasma membrane / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / GPVI-mediated activation cascade / Tie2 Signaling / RAC1 GTPase cycle / phosphotyrosine residue binding / Interleukin-7 signaling / positive regulation of cell adhesion / Downstream signal transduction / B cell differentiation / response to endoplasmic reticulum stress / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of signaling by CBL / Signaling by SCF-KIT / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by ALK fusions and activated point mutants / insulin receptor signaling pathway / DAP12 signaling / protein transport / Downstream TCR signaling / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphatase binding / G alpha (q) signalling events / host cell cytoplasm / Extra-nuclear estrogen signaling / regulation of autophagy / immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / protein heterodimerization activity / focal adhesion / host cell nucleus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Influenza virus non-structural protein, effector domain / 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 ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 domain / Influenza virus non-structural protein, effector domain / 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 / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit beta / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShen, Q. / Zhao, B. / Li, P. / Cho, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127723-01A1 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses.
Authors: Cho, J.H. / Zhao, B. / Shi, J. / Savage, N. / Shen, Q. / Byrnes, J. / Yang, L. / Hwang, W. / Li, P.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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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


Theoretical massNumber of molelcules
Total (without water)72,6354
Polymers72,6354
Non-polymers00
Water55831
1
A: Non-structural protein 1
C: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,3172
Polymers36,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-8 kcal/mol
Surface area15270 Å2
MethodPISA
2
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,3172
Polymers36,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 94.030, 67.220
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16424.043 Da / Num. of mol.: 2 / Mutation: W187R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Strain: A/Brevig Mission/1/1918 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: Q99AU3
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit beta / PtdIns-3-kinase regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit beta / PtdIns-3-kinase regulatory subunit p85-beta


Mass: 19893.389 Da / Num. of mol.: 2 / Fragment: iSH2 domain / Mutation: C501S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00459
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 mM sodium phosphate, 80 mM NaCl

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→64.83 Å / Num. obs: 19133 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.75 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.099 / Rrim(I) all: 0.192 / Net I/σ(I): 6.7 / Num. measured all: 70864 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.75-2.93.70.6231022227740.7610.3790.7312.1100
8.7-64.833.50.12121826230.9610.0770.14512.899.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4Q

3l4q


Resolution: 2.75→44.65 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 901 4.72 %
Rwork0.2281 18202 -
obs0.2296 19103 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.13 Å2 / Biso mean: 60.7838 Å2 / Biso min: 24.17 Å2
Refinement stepCycle: final / Resolution: 2.75→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 0 31 4262
Biso mean---55.73 -
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7501-2.92230.35191610.326630033164
2.9223-3.14790.33591670.290129853152
3.1479-3.46460.30441410.264130273168
3.4646-3.96570.24321570.225130403197
3.9657-4.99530.23051390.189930403179
4.9953-44.65630.23021360.202331073243
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.52890.3998-1.11018.040.54748.3461-0.6684-0.9056-0.57810.45360.4409-0.40860.5311.69830.28170.5210.108-0.01660.48080.03120.41654.879321.646315.1602
24.7260.23174.15266.5138-0.61223.6502-0.4250.35280.71040.48990.06210.2038-0.8595-0.1230.34650.53430.11970.05440.40070.05730.431946.298339.428810.7791
35.72731.18710.97225.49241.60296.92840.0322-0.11940.94590.1175-0.02460.0517-0.69580.46140.00360.3722-0.00220.08350.3918-0.06240.329854.472735.64189.9053
46.9542-0.0295-0.23839.02240.11458.00990.17140.11040.14670.01230.0439-0.5778-0.05020.4499-0.20360.19990.04180.02790.31240.05950.330955.232628.05389.657
57.87745.68491.84376.62514.05718.218-0.65230.19680.4607-1.26360.29510.2497-0.58460.51850.29810.3716-0.0203-0.04560.33010.05180.402653.306332.59881.3118
69.4268-4.23920.8148.44991.0518.8279-0.5502-0.23980.68670.4150.9534-1.025-1.82771.6995-0.26480.5601-0.29110.07530.7851-0.19830.685363.265139.130311.0123
70.07320.7312-0.5282.0056-6.68854.4996-0.91521.4034-2.12641.03410.1132-4.4271-0.01182.8760.43930.5183-0.0814-0.05021.0607-0.19641.283565.635724.68638.2434
86.52191.7219-0.08886.4206-2.17192.84081.3461-0.877-0.31161.619-0.6141-0.7340.9757-0.8674-0.62661.3376-0.4329-0.18821.6234-0.04241.044766.841639.94528.106
96.7923-6.51533.32188.1171-3.49384.1663-0.3209-0.9729-0.31250.65140.6502-0.05120.4050.1179-0.30.86270.01250.00520.6132-0.07740.484460.708-1.917224.5914
103.5544-0.42130.66526.04670.76934.44990.58390.2155-0.7422-1.068-0.00090.25661.23510.2005-0.48360.85410.30850.05930.725-0.020.620666.6383-14.821723.7532
115.5547-0.4591.68737.5071-1.24256.4329-0.1008-0.612-0.08990.9950.2130.28970.0057-0.1442-0.07610.3557-0.04190.01470.38880.00710.29144.562918.924715.8428
123.8057-0.1285-3.03915.28631.69614.38080.2550.5417-0.1799-0.3281-0.2359-0.85890.1920.36960.15110.28790.0210.06480.50180.03470.527145.96937.3917-10.6897
137.90542.06393.67396.15673.53845.93860.0274-0.27090.1020.2383-0.50831.0197-0.0379-0.76430.36340.35470.04750.07170.39310.00390.504127.80667.7165-4.5689
147.05770.86592.72224.83260.95625.18530.0843-0.1113-0.56910.3066-0.02310.17620.63910.2605-0.13380.36560.060.12790.30790.0310.398939.5172.0802-5.0418
155.86743.57284.38648.25183.7298.558-0.11380.1408-0.093-0.6198-0.01840.4564-0.3266-0.32320.10710.21290.0219-0.01720.381900.37735.23778.7401-3.9257
165.51332.48193.43133.65462.16649.7240.2489-0.3486-0.59130.8549-0.1014-0.01270.9205-0.5271-0.18480.54410.04970.06590.37040.08990.578733.8917-2.486-0.0551
178.0471-0.18984.54582.51264.87022.0014-0.1683-1.5474-2.27791.58581.526-0.09453.5269-0.74060.20150.66170.07750.16680.59560.15950.956446.7563-3.9794-1.5883
184.8852-2.1792-2.44022.76721.87573.09350.18440.89410.4249-0.0307-0.0621-0.29940.2437-0.1088-0.04250.4792-0.099-0.03430.55290.04540.47867.2397.8791-19.5055
197.6025-1.976-2.66912.10740.90951.89530.21160.54540.3366-0.293-0.0322-0.4730.10540.2874-0.26810.48110.0282-0.00920.57080.02250.418469.38438.2142-18.2864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 99 )A86 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 112 )A100 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 136 )A113 - 136
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 162 )A137 - 162
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 188 )A163 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 195 )A189 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 201 )A196 - 201
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 212 )A202 - 212
9X-RAY DIFFRACTION9chain 'C' and (resid 433 through 534 )C433 - 534
10X-RAY DIFFRACTION10chain 'C' and (resid 535 through 561 )C535 - 561
11X-RAY DIFFRACTION11chain 'C' and (resid 562 through 597 )C562 - 597
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 99 )B86 - 99
13X-RAY DIFFRACTION13chain 'B' and (resid 100 through 120 )B100 - 120
14X-RAY DIFFRACTION14chain 'B' and (resid 121 through 151 )B121 - 151
15X-RAY DIFFRACTION15chain 'B' and (resid 152 through 170 )B152 - 170
16X-RAY DIFFRACTION16chain 'B' and (resid 171 through 195 )B171 - 195
17X-RAY DIFFRACTION17chain 'B' and (resid 196 through 204 )B196 - 204
18X-RAY DIFFRACTION18chain 'D' and (resid 433 through 497 )D433 - 497
19X-RAY DIFFRACTION19chain 'D' and (resid 498 through 597 )D498 - 597

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