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- PDB-7qrs: Structural insight into the Scribble PDZ domains interaction with... -

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Basic information

Entry
Database: PDB / ID: 7qrs
TitleStructural insight into the Scribble PDZ domains interaction with the oncogenic Human T-cell lymphotrophic virus-1 (HTLV-1) Tax1
Components
  • Protein Tax-1
  • Protein scribble homolog
KeywordsVIRAL PROTEIN / Human T lymphotrophic virus-1 / HTLV-1 / cell polarity / isothermal titration calorimetry / Tax1 / PDZ / scribble
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / 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 ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of receptor recycling / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / regulation of mRNA stability / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / SH3 domain binding / positive regulation of type II interferon production / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / cellular response to lipopolysaccharide / basolateral plasma membrane / host cell cytoplasm / cell population proliferation / postsynaptic density / positive regulation of apoptotic process / cadherin binding / negative regulation of gene expression / protein kinase binding / positive regulation of DNA-templated transcription / host cell nucleus / glutamatergic synapse / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
HTLV Tax / HTLV Tax / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype ...HTLV Tax / HTLV Tax / : / : / 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
ACETATE ION / Protein Tax-1 / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJavorsky, A. / Soares da Costa, T.P. / Mackie, E.R. / Humbert, P.O. / Kvansakul, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Structural insight into the Scribble PDZ domains interaction with the oncogenic Human T-cell lymphotrophic virus-1 (HTLV-1) Tax1 PBM.
Authors: Javorsky, A. / Maddumage, J.C. / Mackie, E.R.R. / Soares da Costa, T.P. / Humbert, P.O. / Kvansakul, M.
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 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: Protein Tax-1
D: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,36412
Polymers26,8584
Non-polymers5058
Water2,720151
1
A: Protein scribble homolog
D: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7577
Polymers13,4292
Non-polymers3285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-6 kcal/mol
Surface area7150 Å2
MethodPISA
2
B: Protein scribble homolog
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6065
Polymers13,4292
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-7 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.257, 50.257, 184.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,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 Protein Tax-1 / Protein X-LOR / Protein PX / Trans-activating transcriptional regulatory protein of HTLV-1


Mass: 1048.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Strain: isolate Caribbea HS-35 subtype A / Gene: tax / Production host: synthetic construct (others) / References: UniProt: P14079
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Zinc chloride, 0.1M Sodium acetate ph5, 20% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→46.1 Å / Num. obs: 25599 / % possible obs: 99.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 31.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.48
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 2557 / CC1/2: 0.43

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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: 1.77→28.14 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2755 1314 5.17 %
Rwork0.2408 24086 -
obs0.2426 25400 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.51 Å2
Refinement stepCycle: LAST / Resolution: 1.77→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 34 151 1814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861673
X-RAY DIFFRACTIONf_angle_d0.97492243
X-RAY DIFFRACTIONf_chiral_restr0.0562249
X-RAY DIFFRACTIONf_plane_restr0.0057304
X-RAY DIFFRACTIONf_dihedral_angle_d7.57091324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.840.38761400.35892691X-RAY DIFFRACTION99.4
1.84-1.920.36371450.33362703X-RAY DIFFRACTION99.65
1.92-2.030.33131540.31712651X-RAY DIFFRACTION99.5
2.03-2.150.37231230.29252708X-RAY DIFFRACTION99.72
2.15-2.320.30931600.27692669X-RAY DIFFRACTION99.89
2.32-2.550.31241700.25812692X-RAY DIFFRACTION99.93
2.55-2.920.2881520.25272656X-RAY DIFFRACTION99.15
2.92-3.680.25231220.22652713X-RAY DIFFRACTION99.79
3.68-28.140.23151480.19952603X-RAY DIFFRACTION95.92

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