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- PDB-7qs9: Structural basis on the interaction of Scribble PDZ domains with ... -

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Basic information

Entry
Database: PDB / ID: 7qs9
TitleStructural basis on the interaction of Scribble PDZ domains with the Tick Born encephalitis virus (TBEV) NS5 protein
Components
  • Protein scribble homolog
  • RNA-directed RNA polymerase NS5
KeywordsVIRAL PROTEIN / Tick Born encephalitis virus / TBEV / cell polarity / isothermal titration calorimetry / NS5 / PDZ / scribble
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / flavivirin / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / signaling adaptor activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / double-stranded RNA binding / positive regulation of type II interferon production / viral capsid / cell-cell junction / cell migration / nucleoside-triphosphate phosphatase / presynapse / cell junction / lamellipodium / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / basolateral plasma membrane / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cell population proliferation / RNA helicase activity / postsynaptic density / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / cadherin binding / induction by virus of host autophagy / positive regulation of apoptotic process / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / glutamatergic synapse / viral envelope / host cell nucleus / virion attachment to host cell / protein kinase binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / : / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...: / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / : / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Leucine rich repeat / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Leucine-rich repeat profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Tick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
C: RNA-directed RNA polymerase NS5
E: RNA-directed RNA polymerase NS5


Theoretical massNumber of molelcules
Total (without water)27,5114
Polymers27,5114
Non-polymers00
Water2,234124
1
A: Protein scribble homolog
C: RNA-directed RNA polymerase NS5


Theoretical massNumber of molelcules
Total (without water)13,7552
Polymers13,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-3 kcal/mol
Surface area5260 Å2
MethodPISA
2
B: Protein scribble homolog
E: RNA-directed RNA polymerase NS5


Theoretical massNumber of molelcules
Total (without water)13,7552
Polymers13,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-3 kcal/mol
Surface area5220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.201, 35.555, 44.981
Angle α, β, γ (deg.)75.597, 85.870, 84.693
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 12792.356 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 RNA-directed RNA polymerase NS5 / Non-structural protein 5


Mass: 963.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tick-borne encephalitis virus
References: UniProt: Q01299, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 0.15m KBr, 30% w/v PEG 2000

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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 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.8→34.33 Å / Num. obs: 55150 / % possible obs: 97.43 % / Redundancy: 3.62 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 1.16 / Num. unique obs: 5642 / CC1/2: 0.53

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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: 5VWC

5vwc


Resolution: 1.8→34.33 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.2011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2874 735 4.85 %
Rwork0.2382 14435 -
obs0.2405 55150 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 0 124 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641432
X-RAY DIFFRACTIONf_angle_d0.71771928
X-RAY DIFFRACTIONf_chiral_restr0.0457218
X-RAY DIFFRACTIONf_plane_restr0.0031257
X-RAY DIFFRACTIONf_dihedral_angle_d2.8428848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.35771520.3022823X-RAY DIFFRACTION95.87
1.94-2.140.40581420.26522889X-RAY DIFFRACTION97.02
2.14-2.440.28311610.24492845X-RAY DIFFRACTION97.34
2.44-3.080.29091410.24622938X-RAY DIFFRACTION98.18
3.08-34.330.2321390.20712940X-RAY DIFFRACTION98.81

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