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

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Basic information

Entry
Database: PDB / ID: 7qrt
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 / : / neurotransmitter receptor transport postsynaptic membrane to endosome / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting ...symbiont-mediated perturbation of host exit from mitosis / : / neurotransmitter receptor transport postsynaptic membrane to endosome / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / extrinsic component of postsynaptic density membrane / 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 / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / 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 / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / 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 / cell migration / cell-cell junction / positive regulation of type II interferon production / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cellular response to lipopolysaccharide / cell population proliferation / host cell cytoplasm / postsynaptic density / cadherin binding / positive regulation of apoptotic process / negative regulation of gene expression / glutamatergic synapse / host cell nucleus / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane
Similarity search - Function
HTLV Tax / HTLV Tax / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain ...HTLV Tax / HTLV Tax / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
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: 1.9 Å
AuthorsJavorsky, A. / Soares da Costa, T.P. / Mackie, E.R. / Humbert, P.O. / Kvansakul, M. / Maddumage, J.C.
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein scribble homolog
B: Protein scribble homolog
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4619
Polymers19,9453
Non-polymers5166
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 ratio stoichiometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-60 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.757, 100.757, 68.525
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-413-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 11 - 100 / Label seq-ID: 1 - 90

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 11 through 101)AA
22chain 'B'BB

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Components

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


Mass: 9448.622 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.: 1 / Source method: obtained synthetically / Source: (synth.) Human T-cell leukemia virus type I / References: UniProt: P14079
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M Ammonium sulfate, 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: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.87→53.89 Å / Num. obs: 17472 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.1
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 1634 / CC1/2: 0.25

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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: 5VWK

5vwk


Resolution: 1.9→53.89 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 840 5.12 %
Rwork0.2131 15577 -
obs0.215 16417 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 26 121 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791432
X-RAY DIFFRACTIONf_angle_d1.15531934
X-RAY DIFFRACTIONf_chiral_restr0.0634221
X-RAY DIFFRACTIONf_plane_restr0.0102252
X-RAY DIFFRACTIONf_dihedral_angle_d16.731838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.33361260.30282523X-RAY DIFFRACTION97.57
2.02-2.170.29651480.26082519X-RAY DIFFRACTION98.38
2.17-2.390.27191240.23032562X-RAY DIFFRACTION98.03
2.39-2.740.27171500.21972564X-RAY DIFFRACTION98.66
2.74-3.450.27451300.21092630X-RAY DIFFRACTION99.03
3.45-53.890.22021620.19612779X-RAY DIFFRACTION98.96
Refinement TLS params.Method: refined / Origin x: 13.6459058815 Å / Origin y: 34.5746104197 Å / Origin z: -0.0372103651259 Å
111213212223313233
T0.304691649077 Å2-0.0283722654435 Å20.0513460006396 Å2-0.327813206708 Å2-0.0121931212303 Å2--0.317690372721 Å2
L0.601576796299 °2-0.239359132921 °20.363597809945 °2-0.909030901207 °2-0.137261298477 °2--1.1381008729 °2
S0.0129731506356 Å °0.102970368722 Å °0.0326544579518 Å °-0.0976062650159 Å °-0.0191726255161 Å °0.0427842079149 Å °0.0199316883483 Å °-0.110105221571 Å °-9.55677059513E-5 Å °
Refinement TLS groupSelection details: all

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