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- PDB-7rch: Crystal structure of NS1-ED of Vietnam influenza A virus in compl... -

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Basic information

Entry
Database: PDB / ID: 7rch
TitleCrystal structure of NS1-ED of Vietnam influenza A virus in complex with the p85-beta-iSH2 domain of human PI3K
Components
  • Non-structural protein 1
  • Phosphatidylinositol 3-kinase regulatory subunit beta
KeywordsVIRAL PROTEIN / Vietnam 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 / IRS-mediated signalling / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / RHOD GTPase cycle / RHOF 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 / IRS-mediated signalling / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of stress fiber assembly / 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 / Regulation of T cell activation by CD28 family / 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 / CD28 dependent PI3K/Akt signaling / 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 / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Role of phospholipids in phagocytosis / Interleukin receptor SHC signaling / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / RAC1 GTPase cycle / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of cell adhesion / Interleukin-7 signaling / Downstream signal transduction / B cell differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / regulation of autophagy / 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 / Downstream TCR signaling / protein transport / insulin receptor signaling pathway / PIP3 activates AKT signaling / DAP12 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / protein heterodimerization activity / focal adhesion / symbiont-mediated suppression of host gene expression / : / host cell nucleus / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 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 ...Phosphatidylinositol 3-kinase regulatory subunit beta, SH3 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 / S15/NS1, RNA-binding
Similarity search - Domain/homology
Non-structural protein 1 / Phosphatidylinositol 3-kinase regulatory subunit beta
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKim, I. / Zhao, B. / Li, P. / Cho, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM127723 01A1 United States
Welch FoundationA-2028-20200401 United States
CitationJournal: Nat Commun / Year: 2022
Title: Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus.
Authors: Kim, I. / Dubrow, A. / Zuniga, B. / Zhao, B. / Sherer, N. / Bastiray, A. / Li, P. / Cho, J.H.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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


Theoretical massNumber of molelcules
Total (without water)68,0254
Polymers68,0254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-28 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 92.840, 67.120
Angle α, β, γ (deg.)90.000, 105.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 14103.206 Da / Num. of mol.: 2 / Fragment: UNP residues 81-206 / Mutation: W182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Viet Nam/1203/2004(H5N1) / Gene: NS1, NS / Production host: Escherichia coli (E. coli) / References: UniProt: A5A5U1
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit beta / PI3-kinase regulatory subunit beta / PI3K regulatory subunit beta / PtdIns-3-kinase regulatory ...PI3-kinase regulatory subunit beta / PI3K regulatory subunit beta / PtdIns-3-kinase regulatory subunit beta / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit beta / PI3-kinase subunit p85-beta / PtdIns-3-kinase regulatory subunit p85-beta


Mass: 19909.453 Da / Num. of mol.: 2 / Fragment: iSH2 (UNP residues 435-597)
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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 278 K / Method: small tubes
Details: 20 mM sodium phosphate, pH 7.0, 80 mM sodium chloride

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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: Jan 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→64.82 Å / Num. obs: 13030 / % possible obs: 99 % / Redundancy: 3.52 % / Biso Wilson estimate: 74.29 Å2 / CC1/2: 0.975 / Net I/σ(I): 4
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 2318 / CC1/2: 0.614

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OX7

6ox7


Resolution: 3.1→50 Å / SU ML: 0.5456 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2762 625 4.8 %
Rwork0.2429 12401 -
obs0.2444 13026 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.95 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 0 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024258
X-RAY DIFFRACTIONf_angle_d0.44695716
X-RAY DIFFRACTIONf_chiral_restr0.0363636
X-RAY DIFFRACTIONf_plane_restr0.0029738
X-RAY DIFFRACTIONf_dihedral_angle_d14.86531658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.34011820.3153022X-RAY DIFFRACTION97
3.41-3.910.32571570.27743072X-RAY DIFFRACTION97.58
3.91-4.920.26111330.22263138X-RAY DIFFRACTION98.23
4.92-500.23781530.21973169X-RAY DIFFRACTION98.6
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)
17.584689559970.8512530429520.9151570617847.54446156417-0.9485431771017.17996888847-0.173621219325-0.6536729294220.8979167800460.6988568549160.1751320613920.135760722088-0.7093246903160.00488944001290.006934801572190.6304366662250.04401267472280.1219942510870.423973622645-0.04436066510270.49982252143820.811871278333.566322658411.4260579017
29.345330581961.855069527961.770398193112.01396484202-1.185959117153.854407533930.03021431417730.5458552393480.58459667650.0385941490091-0.355037181219-0.2427701972690.1794090320730.5326108348080.2947038795350.5056794061420.1648466649910.07447197294370.3937843670990.05820960243940.50301653841624.034293022327.33342142448.35835663534
33.189965531092.335487123783.414071416115.027070446221.203371324574.29120693722-0.9440044164451.371639290190.738954554036-1.640557274191.67013088769-1.35623111681-1.454931715072.56017627973-0.5555751876340.762022270974-0.2405896568420.042520031150.7216141020010.03503499803350.69771577695527.152484270235.25810956051.81141999805
46.55853837223.244744122991.701221198277.005475525454.363093005763.930853993570.81612509120.4526843886290.1452932347450.4914120142020.240448903759-2.85964247193-0.07829623789121.62808066505-1.095127930210.646450299258-0.07649038677330.08105570227071.06720574819-0.1898571339391.0206276828834.552772943832.855029995410.0443978619
51.11690577764-0.3245489316730.3227329712230.572469294575-1.674523445965.30690382582-0.509454076735-0.2307258671330.0904695960772-0.2796136041240.0193125370412-0.0428507011927-0.8762122082541.17626757822-0.9332538924220.341613086161-0.4368462879840.9520112651812.17524793654-0.4381768774581.1734196059136.297246148637.48434450746.39113512372
63.13263862943-2.39329779983-1.19970694124.072946250480.02312959776922.80919553237-0.251138817748-1.28018473088-0.8513429647280.6949597951350.7712199775840.2232500884540.5155021010550.676977238732-0.3926686292890.9310933304470.2592693026210.0132112991460.968033158604-0.100099567130.65339329424928.25669656310.53581428613323.5957475111
71.998912904530.011827590998-0.01105224166670.0179768373716-0.0135940483892.09290478602-0.409547805291-0.364561985794-0.5928242951660.824122250410.5175350754580.2257360379430.4781052159590.651813237101-0.2116051430680.944616927440.3133010566040.06730518380350.764274460184-0.0165198046170.63244619190826.40071028661.7226794863120.4034203753
84.66267070988-0.3237509550221.510632548387.20679752826-2.878099783972.642630356120.7413086114660.2805137095420.531230977441-0.725577354436-0.779146776361-0.4130589416121.07439124929-0.1515000940770.2918869066910.3992133647750.1423006957720.1467892620150.645018947419-0.0856976767010.51165190730215.65550572697.0533901561-10.5625171515
97.294965797534.51441530787-6.230349957872.90336505175-3.846375528525.48946946381-0.0732498813141-0.01297454793061.92264429973-1.07369977650.575801250521.439031749741.502068842990.812079499582-0.545813932510.558553641268-0.000234364889981-0.2679420864671.04142888223-0.1104611599080.930943360115-4.067772709897.76514223894-11.960626112
105.75354826854-1.237410795772.264930984266.51796747505-0.9127884668457.163255999920.314767778716-0.149738305588-0.8338324897280.14384443166-0.07794260371910.6811792243090.505884181042-0.118493318119-0.1760168122840.414004097640.06798379688810.1747349148470.428621650102-0.04230149019440.5085248271565.996376336833.44074833456-3.32341516225
112.280960711391.6940891099-0.07929844274534.59206274802-2.449495543422.480086933260.5586071442170.154525692211-0.4401766172290.261100801663-0.380873121410.1551009442110.0173782086318-0.3132904144-0.04644710437680.4116574697450.185032053401-0.02137136692760.519821974101-0.01991274866140.5436959380554.998641265638.60798695899-3.86873079712
126.78788782791.48049015295-3.70764750158.88939763404-2.088981511823.914676505940.50579514411-0.696907329549-1.473788160531.78701347670.07984158872440.4091932625710.6168260665270.0752157145394-0.08104514914210.5821796829370.05989532099390.1156848980520.2960020466380.04202871986770.8448057080224.88139931761-0.4050022795712.95592224462
131.810399656331.528607856010.4793356046248.18690532374-1.240024704093.25412308698-0.1491633712761.66208089583-2.91258548839-0.9007884963670.03176389170230.5180370831380.564371040598-0.385264002835-0.1655146361310.759224075945-0.00573075979910.09906838580150.835570079493-0.3091675017850.9198967266052.08720665909-7.222968089-6.49816777588
144.99524618169-1.81329607418-4.310979311673.782546891952.84812630614.2522687249-1.96315593895-0.0968078715756-2.678495400310.6237648528421.20432141582-0.06193792030523.443222256150.610231805730.6458576766580.959083897938-0.01831768757020.1052084222430.572765299154-0.05612931321890.8575615724415.8783333825-4.62245359624-1.58270379766
156.09280799221-2.74292867843-1.681099129052.334811656891.349911857333.358375822510.3321546490470.423762364865-0.24365240646-0.4671648152370.0779573557779-0.009744897471810.2356617830930.914064815318-0.2285980043290.6916282385950.1685180044410.03563274930040.88747485471-0.1280590962790.67437275205542.63929364195.72128508085-21.0559192512
166.26088211092-1.19809924176-2.990411081852.676795690531.680002029284.25560457458-0.2115975544740.1730440862210.0788139152592-0.2322191816220.39347920249-0.5239125007030.3478045840610.750485983021-0.1607351435210.5557044755350.06224995773870.1171567222730.492048720951-0.0156613132430.56167572674734.189733355111.1206881754-16.4737995377
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 81 through 121 )AA81 - 1211 - 41
22chain 'A' and (resid 122 through 165 )AA122 - 16542 - 85
33chain 'A' and (resid 166 through 183 )AA166 - 18386 - 103
44chain 'A' and (resid 184 through 195 )AA184 - 195104 - 115
55chain 'A' and (resid 196 through 206 )AA196 - 206116 - 126
66chain 'C' and (resid 433 through 492 )CB433 - 4921 - 60
77chain 'C' and (resid 493 through 597 )CB493 - 59761 - 129
88chain 'B' and (resid 81 through 94 )BC81 - 941 - 14
99chain 'B' and (resid 95 through 101 )BC95 - 10115 - 21
1010chain 'B' and (resid 102 through 146 )BC102 - 14622 - 66
1111chain 'B' and (resid 147 through 165 )BC147 - 16567 - 85
1212chain 'B' and (resid 166 through 182 )BC166 - 18286 - 102
1313chain 'B' and (resid 183 through 190 )BC183 - 190103 - 110
1414chain 'B' and (resid 191 through 199 )BC191 - 199111 - 119
1515chain 'D' and (resid 433 through 527 )DD433 - 5271 - 74
1616chain 'D' and (resid 528 through 597 )DD528 - 59775 - 144

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