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- PDB-7qs8: Structural insight into the Scribble PDZ domains interaction with... -

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Basic information

Entry
Database: PDB / ID: 7qs8
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 / 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 ...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 / 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 / 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 / adherens junction / Asymmetric localization of PCP proteins / neural tube closure / wound healing / cell-cell adhesion / SH3 domain binding / positive regulation of type II interferon production / cell junction / cell-cell junction / cell migration / lamellipodium / presynapse / cellular response to lipopolysaccharide / basolateral plasma membrane / host cell cytoplasm / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / 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
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: 1.85 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 13, 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
C: Protein Tax-1
B: Protein scribble homolog
D: Protein Tax-1


Theoretical massNumber of molelcules
Total (without water)21,7274
Polymers21,7274
Non-polymers00
Water1,35175
1
A: Protein scribble homolog
C: Protein Tax-1


Theoretical massNumber of molelcules
Total (without water)10,8632
Polymers10,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2 kcal/mol
Surface area5060 Å2
MethodPISA
2
B: Protein scribble homolog
D: Protein Tax-1


Theoretical massNumber of molelcules
Total (without water)10,8632
Polymers10,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.389, 43.795, 60.073
Angle α, β, γ (deg.)90.000, 92.399, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYARGARGchain 'A'AA10 - 191 - 10
121PROPROGLYGLYchain 'A'AA23 - 3114 - 22
131PROPROARGARGchain 'A'AA44 - 9035 - 81
141GLUGLUARGARGchain 'A'AA94 - 10185 - 92
251GLYGLYARGARG(chain 'B' and (resid 10 through 21 or resid 23 through 32 or resid 44 through 102))BC10 - 191 - 10
261PROPROGLYGLY(chain 'B' and (resid 10 through 21 or resid 23 through 32 or resid 44 through 102))BC23 - 3114 - 22
271PROPROARGARG(chain 'B' and (resid 10 through 21 or resid 23 through 32 or resid 44 through 102))BC44 - 9035 - 81
281GLUGLUARGARG(chain 'B' and (resid 10 through 21 or resid 23 through 32 or resid 44 through 102))BC94 - 10185 - 92
192HISHISVALVAL(chain 'C' and (resid 11 through 12 or (resid 13...CB11 - 172 - 8
2102HISHISVALVALchain 'D'DD11 - 172 - 8

NCS ensembles :
ID
1
2

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Components

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


Mass: 9815.206 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: obtained synthetically / Source: (synth.) Human T-cell leukemia virus type I / References: UniProt: P14079
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes ph 7, 30% v/v Jeffamine

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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: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→44.22 Å / Num. obs: 16499 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.29 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.3
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 1.32 / Num. unique obs: 1313 / CC1/2: 0.58

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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: 1.85→31.14 Å / SU ML: 0.247 / Cross valid method: FREE R-VALUE / Phase error: 30.8321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 --
Rwork0.2258 15667 -
obs-16499 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 75 1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011310
X-RAY DIFFRACTIONf_angle_d1.1961761
X-RAY DIFFRACTIONf_chiral_restr0.0604210
X-RAY DIFFRACTIONf_plane_restr0.0087232
X-RAY DIFFRACTIONf_dihedral_angle_d11.3963800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.960.3251240.2762293X-RAY DIFFRACTION86.23
1.96-2.110.30371430.23432643X-RAY DIFFRACTION99.93
2.11-2.330.30431370.22022663X-RAY DIFFRACTION100
2.33-2.660.28481390.22152657X-RAY DIFFRACTION100
2.66-3.350.26461400.22352690X-RAY DIFFRACTION100
3.35-31.140.25931490.22362721X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -18.5027413285 Å / Origin y: 1.52310073643 Å / Origin z: -14.4418081372 Å
111213212223313233
T0.223807062696 Å2-0.0073280369172 Å2-0.0371275407 Å2-0.203270419173 Å20.00393348838983 Å2--0.24326842842 Å2
L2.72692390797 °20.0145611281463 °2-0.970897644013 °2-1.97515268433 °20.439686742858 °2--2.61029322039 °2
S0.0309334888991 Å °0.205462860441 Å °-0.0573640428918 Å °-0.0931045229283 Å °0.0709282896189 Å °-0.0678869085546 Å °-0.026978184564 Å °-0.0282139502418 Å °-0.100896779348 Å °
Refinement TLS groupSelection details: all

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