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

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Basic information

Entry
Database: PDB / ID: 7qsa
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 / establishment of T cell polarity / 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 ...extrinsic component of postsynaptic density membrane / establishment of T cell polarity / 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 / 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 / flavivirin / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / 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 / positive regulation of type II interferon production / cell-cell junction / cell junction / viral capsid / cell migration / presynapse / lamellipodium / double-stranded RNA binding / nucleoside-triphosphate phosphatase / basolateral plasma membrane / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cell population proliferation / RNA helicase activity / protein dimerization activity / postsynaptic density / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / positive regulation of apoptotic process / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / protein kinase binding / virion attachment to host cell / host cell nucleus / virion membrane / glutamatergic synapse / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / membrane / 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 / Genome polyprotein, Flavivirus ...: / : / 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 / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / PDZ domain / DEAD box, Flavivirus / Flavivirus DEAD 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 / Roll / 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 / Mainly Beta
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: 2.02 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


Theoretical massNumber of molelcules
Total (without water)20,4473
Polymers20,4473
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, 1:1 ratio stoichiometry in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.947, 69.947, 201.608
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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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: Protein/peptide RNA-directed RNA polymerase NS5 / Non-structural protein 5


Mass: 931.110 Da / Num. of mol.: 1 / 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.: 60 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium nitrate, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350

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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: 2.02→31.02 Å / Num. obs: 12838 / % possible obs: 99.25 % / Redundancy: 12.2 % / Biso Wilson estimate: 42.61 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.1133 / Net I/σ(I): 7.58
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 2401 / CC1/2: 0.51

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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: 5VWI

5vwi


Resolution: 2.02→31.02 Å / SU ML: 0.3246 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2874 --
Rwork0.2527 12112 -
obs-12806 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.71 Å2
Refinement stepCycle: LAST / Resolution: 2.02→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 0 60 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01261261
X-RAY DIFFRACTIONf_angle_d1.341694
X-RAY DIFFRACTIONf_chiral_restr0.0673207
X-RAY DIFFRACTIONf_plane_restr0.012218
X-RAY DIFFRACTIONf_dihedral_angle_d14.2701466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.180.36441260.3012395X-RAY DIFFRACTION99.84
2.18-2.40.28781250.2642391X-RAY DIFFRACTION99.96
2.4-2.740.30871500.26252384X-RAY DIFFRACTION99.8
2.74-3.450.30511430.25962423X-RAY DIFFRACTION99.88
3.46-31.020.26811510.23992519X-RAY DIFFRACTION99.26

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