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- PDB-8cn3: hDLG1-PDZ2 in complex with a TAX1 peptide from HTLV-1 -

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Basic information

Entry
Database: PDB / ID: 8cn3
TitlehDLG1-PDZ2 in complex with a TAX1 peptide from HTLV-1
Components
  • (Disks large homolog 1) x 2
  • GLU-THR-GLU-VAL
KeywordsPROTEIN BINDING / HTLV-1 / Tax-1 / hDLG1 / PBM / protein protein interaction
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / structural constituent of postsynaptic density / GMP kinase activity ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / structural constituent of postsynaptic density / GMP kinase activity / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / reproductive structure development / immunological synapse formation / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / peristalsis / receptor localization to synapse / lateral loop / smooth muscle tissue development / cell projection membrane / bicellular tight junction assembly / cortical microtubule organization / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / hard palate development / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / lens development in camera-type eye / cortical actin cytoskeleton organization / regulation of myelination / Activation of Ca-permeable Kainate Receptor / branching involved in ureteric bud morphogenesis / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / basement membrane / Long-term potentiation / intercalated disc / immunological synapse / lateral plasma membrane / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoskeletal protein binding / negative regulation of T cell proliferation / actin filament polymerization / ionotropic glutamate receptor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / actin filament organization / protein localization to plasma membrane / regulation of membrane potential / positive regulation of protein localization to plasma membrane / adherens junction / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell-cell adhesion / postsynaptic density membrane / sarcolemma / negative regulation of ERK1 and ERK2 cascade / kinase binding / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / nervous system development / regulation of cell shape / RAF/MAP kinase cascade / basolateral plasma membrane / chemical synaptic transmission / molecular adaptor activity / microtubule / transmembrane transporter binding / neuron projection / apical plasma membrane / cadherin binding / membrane raft / positive regulation of cell population proliferation / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell lymphotrophic virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMaseko, S. / Sogues, A. / Volkov, A. / Remaut, H. / Twizere, J.C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)40011260 Belgium
CitationJournal: Antiviral Res. / Year: 2023
Title: Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction.
Authors: Maseko, S.B. / Brammerloo, Y. / Van Molle, I. / Sogues, A. / Martin, C. / Gorgulla, C. / Plant, E. / Olivet, J. / Blavier, J. / Ntombela, T. / Delvigne, F. / Arthanari, H. / El Hajj, H. / ...Authors: Maseko, S.B. / Brammerloo, Y. / Van Molle, I. / Sogues, A. / Martin, C. / Gorgulla, C. / Plant, E. / Olivet, J. / Blavier, J. / Ntombela, T. / Delvigne, F. / Arthanari, H. / El Hajj, H. / Bazarbachi, A. / Van Lint, C. / Salehi-Ashtiani, K. / Remaut, H. / Ballet, S. / Volkov, A.N. / Twizere, J.C.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 1
B: Disks large homolog 1
C: GLU-THR-GLU-VAL
D: GLU-THR-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)25,7174
Polymers25,7174
Non-polymers00
Water34219
1
A: Disks large homolog 1
C: GLU-THR-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)12,8582
Polymers12,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-2 kcal/mol
Surface area5090 Å2
MethodPISA
2
B: Disks large homolog 1
D: GLU-THR-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)12,8602
Polymers12,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-3 kcal/mol
Surface area4960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.349, 53.569, 61.129
Angle α, β, γ (deg.)90.000, 93.330, 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

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Components

#1: Protein Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 12381.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12959
#2: Protein Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 12383.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12959
#3: Protein/peptide GLU-THR-GLU-VAL


Mass: 476.477 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human T-cell lymphotrophic virus type 1 (strain ATK)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 0.075M (NH4)2SO4, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.706→40.26 Å / Num. obs: 4059 / % possible obs: 90.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.15 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.089 / Net I/σ(I): 5.2
Reflection shellResolution: 2.706→2.824 Å / Num. unique obs: 203 / CC1/2: 0.803 / Rpim(I) all: 0.367

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→40.26 Å / SU ML: 0.2956 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2591 197 4.86 %
Rwork0.1865 3856 -
obs0.1901 4053 67.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.08 Å2
Refinement stepCycle: LAST / Resolution: 2.71→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 0 19 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911363
X-RAY DIFFRACTIONf_angle_d1.21451846
X-RAY DIFFRACTIONf_chiral_restr0.0709227
X-RAY DIFFRACTIONf_plane_restr0.0058240
X-RAY DIFFRACTIONf_dihedral_angle_d6.882189

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