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- PDB-7qsb: Structural basis on the interaction of Scribble PDZ domains with ... -

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Basic information

Entry
Database: PDB / ID: 7qsb
TitleStructural basis on the interaction of Scribble PDZ domains with the Tick Born encephalitis virus (TBEV) NS5 protein
ComponentsProtein scribble homolog
KeywordsVIRAL PROTEIN / Tick Born encephalitis virus / TBEV / cell polarity / isothermal titration calorimetry / NS5 / PDZ / scribble
Function / homology
Function and homology information


establishment of T cell polarity / 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 / neurotransmitter receptor transport, endosome to postsynaptic membrane ...establishment of T cell polarity / 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 / 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 / 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 / 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 / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / protein kinase binding / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
: / : / 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. ...: / : / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsJavorsky, A. / Humbert, P.O. / Kvansakul, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2022
Title: Molecular basis of Tick Born encephalitis virus NS5 mediated subversion of apico-basal cell polarity signalling.
Authors: Javorsky, A. / Humbert, P.O. / Kvansakul, M.
History
DepositionJan 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 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


Theoretical massNumber of molelcules
Total (without water)19,5162
Polymers19,5162
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, one peak of Scribble PDZ3
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.882, 60.885, 64.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 9758.154 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.5M Sodium 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: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.84→32.45 Å / Num. obs: 13080 / % possible obs: 99.63 % / Redundancy: 5 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.031 / Net I/σ(I): 9.16
Reflection shellResolution: 1.84→1.91 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 1259 / CC1/2: 0.88

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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: 1.84→31.55 Å / SU ML: 0.2481 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.3091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2924 644 5.01 %
Rwork0.2478 12219 -
obs0.2501 12863 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.98 Å2
Refinement stepCycle: LAST / Resolution: 1.84→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 62 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441206
X-RAY DIFFRACTIONf_angle_d0.60811628
X-RAY DIFFRACTIONf_chiral_restr0.0495199
X-RAY DIFFRACTIONf_plane_restr0.0042214
X-RAY DIFFRACTIONf_dihedral_angle_d20.8112744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.990.39581310.33822386X-RAY DIFFRACTION98.78
1.99-2.190.30631320.27112453X-RAY DIFFRACTION99.38
2.19-2.50.32841170.25682446X-RAY DIFFRACTION99.11
2.5-3.150.30221340.25692430X-RAY DIFFRACTION97.53
3.15-31.550.25951300.22312504X-RAY DIFFRACTION95.19

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