[English] 日本語
Yorodumi
- PDB-8cn1: hDLG1-PDZ1 in complex with a TAX1 peptide from HTLV-1 -

+
Open data


ID or keywords:

Loading...

-
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


regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / endothelial cell proliferation / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / Activation of Ca-permeable Kainate Receptor / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / basement membrane / intercalated disc / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / potassium channel regulator activity / bicellular tight junction / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / cytoskeletal protein binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / postsynaptic density membrane / adherens junction / sarcolemma / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / cell-cell adhesion / kinase binding / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / regulation of cell shape / RAF/MAP kinase cascade / chemical synaptic transmission / basolateral plasma membrane / microtubule / transmembrane transporter binding / molecular adaptor activity / neuron projection / cadherin binding / membrane raft / apical plasma membrane / glutamatergic synapse / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular exosome / nucleus / plasma membrane
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more