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- PDB-8cn1: hDLG1-PDZ1 in complex with a TAX1 peptide from HTLV-1 -

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Basic information

Entry
Database: PDB / ID: 8cn1
TitlehDLG1-PDZ1 in complex with a TAX1 peptide from HTLV-1
Components
  • Disks large homolog 1
  • 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 / hard palate development / GMP kinase activity / structural constituent of postsynaptic density ...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 / hard palate development / GMP kinase activity / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / NrCAM interactions / astral microtubule organization / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / reproductive structure development / immunological synapse formation / lateral loop / receptor localization to synapse / myelin sheath abaxonal region / peristalsis / regulation of sodium ion transmembrane transport / smooth muscle tissue development / bicellular tight junction assembly / cortical microtubule organization / cell projection membrane / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / regulation of ventricular cardiac muscle cell action potential / positive regulation of potassium ion transport / Trafficking of AMPA receptors / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / cortical actin cytoskeleton organization / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / 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 / Long-term potentiation / basement membrane / immunological synapse / intercalated disc / bicellular tight junction / lateral plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / potassium channel regulator activity / phosphatase binding / T cell proliferation / cytoskeletal protein binding / ionotropic glutamate receptor binding / negative regulation of T cell proliferation / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization / protein localization to plasma membrane / regulation of membrane potential / adherens junction / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / neuromuscular junction / sarcolemma / cell-cell adhesion / cytoplasmic side of plasma membrane / kinase binding / negative regulation of epithelial cell proliferation / cell junction / cell-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 / cadherin binding / apical plasma membrane / membrane raft / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / 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 / Pdz3 Domain / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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

Downloads & links

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Assembly

Deposited unit
B: Disks large homolog 1
A: Disks large homolog 1
C: Disks large homolog 1
D: Disks large homolog 1
E: Disks large homolog 1
F: Disks large homolog 1
G: Disks large homolog 1
H: Disks large homolog 1
I: Disks large homolog 1
J: Disks large homolog 1
K: Disks large homolog 1
L: Disks large homolog 1
V: GLU-THR-GLU-VAL
W: GLU-THR-GLU-VAL
X: GLU-THR-GLU-VAL
Y: GLU-THR-GLU-VAL
N: GLU-THR-GLU-VAL
O: GLU-THR-GLU-VAL
P: GLU-THR-GLU-VAL
Q: GLU-THR-GLU-VAL
R: GLU-THR-GLU-VAL
T: GLU-THR-GLU-VAL
Z: GLU-THR-GLU-VAL
U: GLU-THR-GLU-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,87033
Polymers156,00524
Non-polymers8659
Water11,313628
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22050 Å2
ΔGint-165 kcal/mol
Surface area56900 Å2
Unit cell
Length a, b, c (Å)53.537, 82.905, 87.784
Angle α, β, γ (deg.)64.104, 90.137, 89.869
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 12523.976 Da / Num. of mol.: 12
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/peptide
GLU-THR-GLU-VAL


Mass: 476.477 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Human T-cell leukemia virus type I
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5, 0.18 M (NH4)2SO4, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→78.96 Å / Num. obs: 49749 / % possible obs: 89.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.93 Å2 / CC1/2: 0.99 / Net I/σ(I): 4.4
Reflection shellResolution: 2.09→2.347 Å / Rmerge(I) obs: 0.564 / Num. unique obs: 2488 / CC1/2: 0.742 / Rpim(I) all: 0.35 / Rrim(I) all: 0.665 / % possible all: 10.4

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→45.25 Å / SU ML: 0.2719 / Cross valid method: FREE R-VALUE / Phase error: 30.5151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2599 5.23 %
Rwork0.1991 47121 -
obs0.2016 49720 61.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.74 Å2
Refinement stepCycle: LAST / Resolution: 2.09→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8982 0 45 628 9655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779091
X-RAY DIFFRACTIONf_angle_d0.905312260
X-RAY DIFFRACTIONf_chiral_restr0.06031434
X-RAY DIFFRACTIONf_plane_restr0.0081614
X-RAY DIFFRACTIONf_dihedral_angle_d6.21231303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.341950.20240X-RAY DIFFRACTION1.05
2.13-2.170.2085110.225147X-RAY DIFFRACTION3.85
2.17-2.210.237380.2197344X-RAY DIFFRACTION8.35
2.21-2.260.3785200.2142313X-RAY DIFFRACTION7.79
2.26-2.310.3214580.2223824X-RAY DIFFRACTION20.81
2.31-2.370.2982960.22191074X-RAY DIFFRACTION27.63
2.37-2.430.2508930.24141523X-RAY DIFFRACTION37.74
2.43-2.50.27811120.25692030X-RAY DIFFRACTION50.61
2.5-2.580.26491590.25912575X-RAY DIFFRACTION64.15
2.59-2.680.28931640.25133022X-RAY DIFFRACTION74.89
2.68-2.780.30751660.2423526X-RAY DIFFRACTION87.55
2.78-2.910.29241870.24153951X-RAY DIFFRACTION97.34
2.91-3.060.25411540.22094020X-RAY DIFFRACTION98.58
3.06-3.260.28692520.21643920X-RAY DIFFRACTION98.63
3.26-3.510.23812150.18784024X-RAY DIFFRACTION98.72
3.51-3.860.23842150.17443951X-RAY DIFFRACTION98.42
3.86-4.420.20992590.15693943X-RAY DIFFRACTION98.62
4.42-5.560.20761870.15863985X-RAY DIFFRACTION98.4
5.57-45.250.2172380.20153909X-RAY DIFFRACTION97.39
Refinement TLS params.Method: refined / Origin x: -13.528041418 Å / Origin y: 5.9598238844 Å / Origin z: -35.3726593667 Å
111213212223313233
T0.110763791126 Å20.00207585471149 Å2-0.00128315563294 Å2-0.108156416992 Å20.00149783789672 Å2--0.107169862167 Å2
L0.063370837494 °20.0152880988607 °2-0.00927775778194 °2-0.0470626833479 °2-0.0146238595134 °2--0.0117503326087 °2
S0.00689377870847 Å °-0.0109297410782 Å °0.0180223867153 Å °-0.0118661044493 Å °-0.00752097414583 Å °0.00509432991515 Å °-0.00698617193465 Å °-0.018253816332 Å °-9.16470475019E-7 Å °
Refinement TLS groupSelection details: { B|17-109 }

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