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- PDB-6u28: Crystal structure of 1918 NS1-ED W187A in complex with the p85-be... -

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Basic information

Entry
Database: PDB / ID: 6u28
TitleCrystal structure of 1918 NS1-ED W187A in complex with the p85-beta-iSH2 domain of human PI3K
Components
  • Non-structural protein 1
  • Phosphatidylinositol 3-kinase regulatory subunit beta
KeywordsVIRAL PROTEIN / 1918 influenza A virus / NS1 / PI3K
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / IRS-mediated signalling / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of actin filament polymerization / 1-phosphatidylinositol-3-kinase regulator activity / IRS-mediated signalling / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / Co-stimulation by ICOS / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / RHOF GTPase cycle / 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 / RET signaling / CDC42 GTPase cycle / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / T cell differentiation / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / Interleukin receptor SHC signaling / protein serine/threonine kinase inhibitor activity / Role of phospholipids in phagocytosis / 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 / negative regulation of MAPK cascade / Tie2 Signaling / phosphotyrosine residue binding / RAC1 GTPase cycle / positive regulation of cell adhesion / Downstream signal transduction / Interleukin-7 signaling / B cell differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / response to endoplasmic reticulum stress / Regulation of signaling by CBL / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by SCF-KIT / receptor tyrosine kinase binding / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / 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 / Downstream TCR signaling / PIP3 activates AKT signaling / protein transport / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (q) signalling events / host cell cytoplasm / Extra-nuclear estrogen signaling / immune response / regulation of autophagy / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / symbiont-mediated suppression of host gene expression / 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 / Src homology 3 domains / SH2 domain superfamily / 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: 2.95 Å
AuthorsCho, J.H. / Zhao, B. / Savage, N. / Li, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM127723 01A1 United States
National Institute of Food and Agriculture (NIFA, United States)1020344 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
DepositionAug 19, 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

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


Theoretical massNumber of molelcules
Total (without water)72,4634
Polymers72,4634
Non-polymers00
Water00
1
A: Non-structural protein 1
C: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,2312
Polymers36,2312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area15040 Å2
MethodPISA
2
B: Non-structural protein 1
D: Phosphatidylinositol 3-kinase regulatory subunit beta


Theoretical massNumber of molelcules
Total (without water)36,2312
Polymers36,2312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.190, 92.390, 66.940
Angle α, β, γ (deg.)90.000, 105.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16337.927 Da / Num. of mol.: 2 / Fragment: effector domain / Mutation: W187A
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 / 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

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.1 / Details: tris 20 mM, trehalose 0.7 M, sodium chloride 80 mM

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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: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→64.61 Å / Num. obs: 15268 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.87 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.111 / Rrim(I) all: 0.211 / Net I/σ(I): 6.1 / Num. measured all: 53699 / Scaling rejects: 104
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
2.95-3.133.50.938864624550.5980.5871.111.3100
8.85-64.613.30.12519305920.9450.080.1491399.2

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OX7

6ox7


Resolution: 2.95→34.145 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.2395 701 4.61 %
Rwork0.2225 --
obs0.2233 15214 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.18 Å2 / Biso mean: 74.0454 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: final / Resolution: 2.95→34.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 0 0 4219
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.9503-3.17790.30881370.31782892
3.1779-3.49740.29381450.27192858
3.4974-4.00290.27341280.22742902
4.0029-5.04060.21781550.19352909
5.0406-34.1450.20431360.20092952
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)
10.06180.1745-0.20830.7006-0.5910.5445-0.1707-0.7407-0.50460.4328-0.2556-0.0339-0.15950.6275-0.00190.64710.0705-0.02520.49650.05540.492124.56621.453715.0104
20.8492-0.4979-0.2961.0735-0.4770.7928-0.3212-0.02540.85360.31050.2720.2149-0.6211-0.2075-0.00230.62330.1245-0.06240.4311-0.04450.538818.607339.70569.6145
31.0192-0.15690.30870.3874-0.51420.7974-0.22510.1046-0.0390.0442-0.05970.00280.02220.7075-0.00020.44980.0722-0.02770.44130.00110.486927.071325.27838.4362
40.99760.7463-0.53492.1398-0.07241.1173-0.2974-0.10340.2478-0.00360.1829-0.2273-0.3040.3648-0.00010.5128-0.0003-0.0090.4301-0.04560.527826.233232.36356.3605
5-0.01650.0186-0.00940.06410.0412-0.0108-0.2685-0.1378-0.66920.77710.44570.5709-0.20070.17440.00061.3519-0.2385-0.11261.6916-0.05671.037536.680739.45427.9024
60.2764-0.6001-0.39550.98210.03520.9992-0.2407-0.6031-0.34870.36780.46830.38820.2237-0.09390.01160.79360.15190.03170.6533-0.02330.568826.2772.064223.1158
70.52640.51430.09620.7949-0.40080.49720.2189-0.1292-0.42820.3199-0.02910.5529-0.11430.182601.09880.3432-0.03510.8049-0.11150.70641.7016-17.49526.1572
80.80160.66090.49291.3988-0.81072.0302-0.10990.06350.20250.56270.0553-0.0805-0.1225-0.33910.00030.51880.0930.01370.4738-0.04910.451614.23418.85915.7217
90.33210.4226-0.3350.9267-0.15040.50850.30220.9472-0.4476-0.4842-0.062-0.6236-0.02290.16660.00050.41580.04350.03750.6038-0.09410.562615.48977.3079-10.5836
101.9223-1.07510.43880.598-0.28660.1169-0.01380.2015-0.401-0.00110.05770.9314-0.0626-0.27450.00020.5528-0.03020.05620.6318-0.02930.7035-3.66415.2714-5.3868
110.3559-0.2125-0.22580.11520.11060.15420.12980.2049-0.4476-0.01820.1156-0.2630.38790.077800.42350.11950.0140.5765-0.04560.500412.0711.63-5.9498
120.8564-0.3367-0.79481.0833-0.01210.8480.0158-0.05940.09940.3643-0.25350.04350.61410.1309-00.54950.05110.0120.5218-0.00670.4379.02214.4392-5.4754
130.9829-0.36510.84410.8938-0.3171.0003-0.0424-0.2343-0.41120.44740.02480.21360.339-0.36220.00010.4608-0.0123-0.00710.40570.03470.44024.74672.02880.9384
140.1572-0.0627-0.00280.0538-0.11140.3393-0.14110.2383-1.12590.34290.5983-1.0211.2858-0.20080.01170.78970.04430.05060.48290.00690.795216.111-4.0163-1.4274
151.3955-0.0175-0.36510.02990.13531.01280.1730.36870.4614-0.07950.0405-0.20310.05630.04020.00020.58310.0117-0.01210.63610.00130.517340.97015.8633-20.5082
160.8956-0.3142-1.21520.59760.72871.1665-0.03430.2024-0.0192-0.18440.2246-0.10510.02420.21110.00160.44-0.00150.02930.5814-0.05690.472235.295810.4162-16.982
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 126 )A100 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 151 )A127 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 201 )A152 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 212 )A202 - 212
6X-RAY DIFFRACTION6chain 'C' and (resid 433 through 489 )C433 - 489
7X-RAY DIFFRACTION7chain 'C' and (resid 490 through 561 )C490 - 561
8X-RAY DIFFRACTION8chain 'C' and (resid 562 through 597 )C562 - 597
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 99 )B86 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 126 )B100 - 126
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 137 )B127 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 162 )B138 - 162
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 195 )B163 - 195
14X-RAY DIFFRACTION14chain 'B' and (resid 196 through 204 )B196 - 204
15X-RAY DIFFRACTION15chain 'D' and (resid 433 through 525 )D433 - 525
16X-RAY DIFFRACTION16chain 'D' and (resid 526 through 597 )D526 - 597

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