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- PDB-7qtp: Structural biology of the NS1 avian influenza protein subversion ... -

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Basic information

Entry
Database: PDB / ID: 7qtp
TitleStructural biology of the NS1 avian influenza protein subversion on the Scribble cell polarity module
Components
  • Non-structural protein 1
  • Protein scribble homolog
KeywordsVIRAL PROTEIN / Influenza A virus / bird-flu / H5N1 / cell polarity / isothermal titration calorimetry / NS1 / PDZ / scribble
Function / homology
Function and homology information


establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / apoptotic process involved in morphogenesis / cochlear nucleus development / establishment of apical/basal cell polarity / astrocyte cell migration / Scrib-APC-beta-catenin complex / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance ...establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / apoptotic process involved in morphogenesis / cochlear nucleus development / establishment of apical/basal cell polarity / astrocyte cell migration / Scrib-APC-beta-catenin complex / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance / symbiont-mediated suppression of host PKR/eIFalpha signaling / neurotransmitter receptor transport, endosome to postsynaptic membrane / myelin sheath abaxonal region / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / post-anal tail morphogenesis / activation of GTPase activity / auditory receptor cell stereocilium organization / protein serine/threonine kinase inhibitor activity / : / RND2 GTPase cycle / RND3 GTPase cycle / extrinsic component of postsynaptic density membrane / positive regulation of receptor recycling / regulation of postsynaptic neurotransmitter receptor internalization / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / negative regulation of activated T cell proliferation / RHOQ GTPase cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / signaling adaptor activity / adherens junction / Asymmetric localization of PCP proteins / neural tube closure / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell junction / cell-cell junction / cell migration / lamellipodium / presynapse / basolateral plasma membrane / host cell cytoplasm / cell population proliferation / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / positive regulation of apoptotic process / symbiont-mediated suppression of host gene expression / protein kinase binding / host cell nucleus / glutamatergic synapse / RNA binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / S15/NS1, RNA-binding
Similarity search - Domain/homology
Protein scribble homolog / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
H5N1 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJavorsky, A. / Humbert, P.O. / Kvansakul, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2022
Title: Structural Basis of the Avian Influenza NS1 Protein Interactions with the Cell Polarity Regulator Scribble.
Authors: Javorsky, A. / Humbert, P.O. / Kvansakul, M.
History
DepositionJan 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Protein scribble homolog
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)13,5462
Polymers13,5462
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 ratio stoichiometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-3 kcal/mol
Surface area5140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.535, 51.202, 27.868
Angle α, β, γ (deg.)90.000, 90.550, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-941-

HOH

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Components

#1: Protein Protein scribble homolog / Scribble / hScrib / Protein LAP4


Mass: 12380.901 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli (E. coli) / References: UniProt: Q14160
#2: Protein/peptide Non-structural protein 1 / NS1


Mass: 1165.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) H5N1 subtype (virus) / References: UniProt: Q6B3P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.5M Ammonium nitrate, 0.1M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→38.54 Å / Num. obs: 6533 / % possible obs: 99.54 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05011 / Net I/σ(I): 17.74
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.23 / Num. unique obs: 627 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
PHASER1.15.2-3472-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 1.9→38.54 Å / SU ML: 0.2791 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 --
Rwork0.2758 6215 -
obs-6529 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms684 0 0 43 727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061688
X-RAY DIFFRACTIONf_angle_d0.9922
X-RAY DIFFRACTIONf_chiral_restr0.0488106
X-RAY DIFFRACTIONf_plane_restr0.0063121
X-RAY DIFFRACTIONf_dihedral_angle_d17.4274252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.390.3531420.34053088X-RAY DIFFRACTION99.23
2.39-38.540.26291720.25783127X-RAY DIFFRACTION99.85
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)
16.748673987611.0916778917-1.011532536443.1479324524-0.6275823126146.64468581818-0.1757200577911.36528794702-1.19542726402-2.23209980132-0.3009817226020.93387007243-1.04586499416-0.1341124183970.3365156258820.2962605057510.0974287201792-0.3923802808940.412140424009-0.1967047896230.66454281940515.7608172367-15.7789484708-5.68760927969
29.83538386543-0.04923484903380.1034720187375.13140904912-0.3796865535444.35729778036-1.49937007199-1.15911108793-1.220878055171.664103386350.2684329062541.483528729290.728722740614-0.2485544638770.6451508411150.907446545980.1025025396440.3165095916660.297388323889-0.03194804521070.74972259557111.9226718636-16.46916940999.33872113319
38.09389931669-4.898516063521.248695860378.09541465539-0.1078559163495.65383325231-1.24223839114-0.6650573883861.783025538621.677585064640.72792352232-1.456675970370.09580918049341.2772614890.4437786846050.6558057744520.137093211613-0.1341079923760.537467698426-0.09100894164990.24321624432822.7865220174-9.582171303027.38820851659
45.20603469672-1.011723189721.42103285261.66916661166-2.662472461724.62534869271-0.822665573121-0.313672743708-1.805563211591.37402641016-0.1143660523522.130209184731.70067117885-0.5393643490520.4780460944840.606371886973-0.08632580083050.3999125073660.351146175209-0.0662905110340.76721098023512.7326920377-22.95793974763.96943850724
56.03647183077-5.05421663786-1.372445853748.503690702441.213173830342.20775482573-0.05705376743850.4170597520430.8041189105190.209506327469-0.634568291581.26253626173-0.641505309323-0.1897087005450.4121760438070.3262652040670.0294052869017-0.04768690968010.258416366581-0.02538252101980.37443876373812.7871844958-5.532297185671.77674809913
69.09264660677-3.119696410012.543875037222.027995805041.226182815749.35825775619-1.51914902854-1.58733173755-0.1956736531673.01645371290.5300585482011.48722501927-0.57399165669-0.8287362284620.4631877163740.6247558022950.1429345376710.08936292713040.424474212249-0.07207166121980.31896670803910.2691970133-6.2486754239710.9453906637
74.94470096365-4.42717870427-1.103686999755.299393270860.8965215254875.20613226667-0.4130006521721.06233046631-0.2737847937250.209620406-0.1495046038721.198947448150.00498133371959-0.559438191650.3636042361230.1987581315440.0635646648174-0.008321001993270.33385827901-0.02332968488480.56360870265311.3653564659-12.9104699554-1.04221949142
84.91102886175-2.143731374682.131852366194.99271930862-0.567710678697.13918332415-0.112132310506-0.412205001428-0.4007671833341.612961135831.06306421549-0.22727256697-0.4065774745310.352814743981-0.4583005076341.520375242340.5059106599770.05533040016320.6224252634530.1663979483630.26974994664815.1968243965-13.897734327914.5968929874
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 722 through 731 )AA722 - 7311 - 10
22chain 'A' and (resid 732 through 744 )AA732 - 74411 - 19
33chain 'A' and (resid 745 through 763 )AA745 - 76320 - 38
44chain 'A' and (resid 764 through 778 )AA764 - 77839 - 53
55chain 'A' and (resid 779 through 792 )AA779 - 79254 - 67
66chain 'A' and (resid 793 through 801 )AA793 - 80168 - 76
77chain 'A' and (resid 802 through 814 )AA802 - 81477 - 88
88chain 'B' and (resid 257 through 261 )BB257 - 2611 - 5

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