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

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Basic information

Entry
Database: PDB / ID: 7qto
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 / 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: 3.5 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

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Assembly

Deposited unit
A: Protein scribble homolog
B: Protein scribble homolog
C: Non-structural protein 1
D: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)26,5724
Polymers26,5724
Non-polymers00
Water00
1
A: Protein scribble homolog
D: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)13,2862
Polymers13,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein scribble homolog
C: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)13,2862
Polymers13,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.909, 57.009, 61.598
Angle α, β, γ (deg.)90.000, 117.372, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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


Mass: 12380.901 Da / Num. of mol.: 2
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: 904.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) H5N1 subtype (virus) / References: UniProt: Q6DP93

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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: 0.2M Ammonium sulfate, 30% w/v PEG 4000

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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: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.5→30.74 Å / Num. obs: 4238 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 43.7 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.5
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.21 / Num. unique obs: 429 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 3.5→30.74 Å / SU ML: 0.1291 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2657 108 4.91 %
Rwork0.2423 2092 -
obs0.2437 4238 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 0 0 1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231430
X-RAY DIFFRACTIONf_angle_d0.55081922
X-RAY DIFFRACTIONf_chiral_restr0.0456231
X-RAY DIFFRACTIONf_plane_restr0.0022248
X-RAY DIFFRACTIONf_dihedral_angle_d9.0226853
LS refinement shellResolution: 3.5→3.83 Å
RfactorNum. reflection% reflection
Rfree0.2657 108 -
Rwork0.2423 2092 -
obs--97.56 %
Refinement TLS params.Method: refined / Origin x: 6.84195721035 Å / Origin y: -3.87096490399 Å / Origin z: 14.9148275005 Å
111213212223313233
T0.195021377325 Å2-0.0199292083222 Å2-0.00399378976404 Å2-0.218702808679 Å2-0.0345567038678 Å2--0.190928420544 Å2
L1.06679605375 °20.205299986046 °20.438287289438 °2-0.112680479104 °2-0.0605410157013 °2--0.451614104685 °2
S-0.021877115064 Å °0.0039378874925 Å °-0.332522422448 Å °-0.12360910463 Å °-0.0363102378332 Å °-0.0540413443087 Å °-0.146883180043 Å °-0.0824160775525 Å °-0.0447916264783 Å °
Refinement TLS groupSelection details: all

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