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

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Basic information

Entry
Database: PDB / ID: 7qtu
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


extrinsic component of postsynaptic density membrane / establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / symbiont-mediated suppression of host PKR/eIFalpha signaling / mammary gland duct morphogenesis / cell-cell contact zone / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / protein localization to adherens junction / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / receptor clustering / negative regulation of activated T cell proliferation / RHOJ GTPase cycle / RHOQ GTPase cycle / positive regulation of receptor recycling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / CDC42 GTPase cycle / immunological synapse / protein serine/threonine kinase inhibitor activity / synaptic vesicle endocytosis / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / basolateral plasma membrane / host cell cytoplasm / cell population proliferation / postsynaptic density / positive regulation of apoptotic process / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / 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 / PDZ domain / Pdz3 Domain ...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 / PDZ domain / Pdz3 Domain / 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 / Roll / Mainly Beta
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: 2.84 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 16, 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

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Assembly

Deposited unit
B: Protein scribble homolog
D: Non-structural protein 1
A: Protein scribble homolog
C: Non-structural protein 1
E: Protein scribble homolog
F: Non-structural protein 1
G: Protein scribble homolog
H: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)44,1518
Polymers44,1518
Non-polymers00
Water00
1
B: Protein scribble homolog
D: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)11,0382
Polymers11,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area5130 Å2
MethodPISA
2
A: Protein scribble homolog
C: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)11,0382
Polymers11,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-4 kcal/mol
Surface area5480 Å2
MethodPISA
3
E: Protein scribble homolog
F: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)11,0382
Polymers11,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-5 kcal/mol
Surface area5230 Å2
MethodPISA
4
G: Protein scribble homolog
H: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)11,0382
Polymers11,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-3 kcal/mol
Surface area5420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.836, 77.716, 64.752
Angle α, β, γ (deg.)90.000, 94.161, 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

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Components

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


Mass: 9872.258 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Source: (synth.) H5N1 subtype (virus) / References: UniProt: Q6B3P2

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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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium Cacodylate pH4.2, 40% MPD

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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: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.84→42.94 Å / Num. obs: 8916 / % possible obs: 96.9 % / Redundancy: 3 % / Biso Wilson estimate: 56.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.6
Reflection shellResolution: 2.84→2.99 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 864 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
PHASER1.15.2-3472-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWI

5vwi


Resolution: 2.84→42.94 Å / SU ML: 0.312 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.296 --
Rwork0.252 8492 -
obs-8909 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 0 0 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442607
X-RAY DIFFRACTIONf_angle_d0.75713502
X-RAY DIFFRACTIONf_chiral_restr0.0497428
X-RAY DIFFRACTIONf_plane_restr0.0064457
X-RAY DIFFRACTIONf_dihedral_angle_d13.74671608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.250.3271200.30342844X-RAY DIFFRACTION96.64
3.25-4.090.27861500.25552820X-RAY DIFFRACTION97.67
4.09-42.940.28761470.23382828X-RAY DIFFRACTION95.66

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