[English] 日本語
Yorodumi
- PDB-2kaw: NMR structure of the mDvl1 PDZ domain in complex with its inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kaw
TitleNMR structure of the mDvl1 PDZ domain in complex with its inhibitor
ComponentsSegment polarity protein dishevelled homolog DVL-1
KeywordsSIGNALING PROTEIN / INHIBITOR OF PROTEIN-PROTEIN INTERACTIONS / PROTEIN STRUCTURE / PDZ DOMAIN / WNT SIGNALING / Developmental protein / Wnt signaling pathway
Function / homology
Function and homology information


WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL / protein localization to microtubule / positive regulation of neuron projection arborization / RHO GTPases Activate Formins / presynapse assembly / collateral sprouting / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / Wnt signalosome / dendrite morphogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of postsynapse organization / clathrin-coated vesicle / regulation of synaptic vesicle exocytosis / neuromuscular junction development / heart looping / outflow tract morphogenesis / neuronal dense core vesicle / receptor clustering / synaptic vesicle exocytosis / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / lateral plasma membrane / canonical Wnt signaling pathway / prepulse inhibition / cytoplasmic microtubule organization / axonogenesis / negative regulation of protein phosphorylation / axon guidance / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / small GTPase binding / beta-catenin binding / Wnt signaling pathway / positive regulation of neuron projection development / regulation of protein localization / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / intracellular signal transduction / neuron projection / positive regulation of protein phosphorylation / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-SUZ / Segment polarity protein dishevelled homolog DVL-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, HADDOCK
AuthorsLee, H.J. / Shao, Y. / Wang, N.X. / Shi, D.L. / Zheng, J.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Sulindac inhibits canonical Wnt signaling by blocking the PDZ domain of the protein Dishevelled.
Authors: Lee, H.J. / Wang, N.X. / Shi, D.L. / Zheng, J.J.
History
DepositionNov 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9892
Polymers9,6331
Non-polymers3561
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000LOWEST ENERGY CONFORMATION
RepresentativeModel #1lowest energy

-
Components

#1: Protein Segment polarity protein dishevelled homolog DVL-1 / Dishevelled-1 / DSH homolog 1


Mass: 9632.888 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 248-337, PDZ DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dvl1, Dvl / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / References: UniProt: P51141
#2: Chemical ChemComp-SUZ / [(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid / SULINDAC / Sulindac


Mass: 356.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FO3S / Comment: antiinflammatory*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-F1 HALF FILTERED F2 EDIT
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D CBCA(CO)NH
1513D HNCO
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING BASED ON A TOTAL OF 55 RESTRAINTS: 45 INTERMOLECULAR DISTANCE CONTRAINTS, 7 INTRAMOLECULAR DISTANCE CONTRAINTS FOR SMALL MOLECULE, AND 3 ARE ...Text: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING BASED ON A TOTAL OF 55 RESTRAINTS: 45 INTERMOLECULAR DISTANCE CONTRAINTS, 7 INTRAMOLECULAR DISTANCE CONTRAINTS FOR SMALL MOLECULE, AND 3 ARE DISTANCE RESTRAINTS FROM HYDROGEN BONDS

-
Sample preparation

DetailsContents: 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: PDZ / Isotopic labeling: [U-90% 15N, 13C]
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: AMBIENT / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE6001
BRUKER AVANCEBrukerAVANCE8002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
HADDOCK1.2Dominguez, Boelens, Bonvinstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPAKY3.1Goddardchemical shift assignment
HADDOCK1.2Dominguez, Boelens, Bonvinrefinement
RefinementMethod: simulated annealing, HADDOCK / Software ordinal: 1 / Details: NOE distance violation (<0.5A)
NMR constraintsNOE constraints total: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY CONFORMATION / Conformers calculated total number: 2000 / Conformers submitted total number: 20

+
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