[English] 日本語
Yorodumi
- PDB-2lty: NEDD4L WW2 domain in complex with a Smad7 derived peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lty
TitleNEDD4L WW2 domain in complex with a Smad7 derived peptide
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Smad7 derived peptide
KeywordsPROTEIN BINDING/PEPTIDE / WW / NEDD4L / SMAD7 / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / positive regulation of caveolin-mediated endocytosis / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of T cell cytokine production / negative regulation of sodium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / heteromeric SMAD protein complex ...positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / positive regulation of caveolin-mediated endocytosis / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of T cell cytokine production / negative regulation of sodium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / heteromeric SMAD protein complex / regulation of potassium ion transmembrane transporter activity / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of potassium ion transmembrane transport / negative regulation of T-helper 17 cell differentiation / regulation of transforming growth factor beta receptor signaling pathway / response to laminar fluid shear stress / activin receptor binding / negative regulation of protein localization to cell surface / positive regulation of cell-cell adhesion / regulation of epithelial to mesenchymal transition / regulation of membrane repolarization / regulation of sodium ion transmembrane transport / regulation of membrane depolarization / negative regulation of transcription by competitive promoter binding / negative regulation of ubiquitin-protein transferase activity / Signaling by BMP / type I transforming growth factor beta receptor binding / positive regulation of dendrite extension / SMAD protein signal transduction / potassium channel inhibitor activity / negative regulation of activin receptor signaling pathway / adherens junction assembly / sodium channel inhibitor activity / HECT-type E3 ubiquitin transferase / ventricular cardiac muscle cell action potential / protein-containing complex localization / regulation of monoatomic ion transmembrane transport / I-SMAD binding / negative regulation of ossification / transcription regulator inhibitor activity / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / ventricular septum morphogenesis / regulation of dendrite morphogenesis / negative regulation of SMAD protein signal transduction / negative regulation of peptidyl-serine phosphorylation / negative regulation of peptidyl-threonine phosphorylation / protein monoubiquitination / negative regulation of BMP signaling pathway / regulation of cardiac muscle contraction / ubiquitin-like ligase-substrate adaptor activity / anatomical structure morphogenesis / sodium channel regulator activity / potassium channel regulator activity / protein K48-linked ubiquitination / cellular response to transforming growth factor beta stimulus / negative regulation of protein ubiquitination / collagen binding / multivesicular body / transforming growth factor beta receptor signaling pathway / regulation of membrane potential / Downregulation of TGF-beta receptor signaling / negative regulation of cell migration / cellular response to leukemia inhibitory factor / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / regulation of protein stability / Budding and maturation of HIV virion / Stimuli-sensing channels / beta-catenin binding / fibrillar center / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / transcription corepressor activity / Interferon gamma signaling / UCH proteinases / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein stabilization / Ub-specific processing proteases / protein ubiquitination / centrosome / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / E3 ubiquitin-protein ligase, SMURF1 type / SMAD-like domain superfamily / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / SMAD/FHA domain superfamily / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 7 / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Xi, Q. / Lopes, T. / Gao, S. / Massague, J.
CitationJournal: Structure / Year: 2012
Title: Structural Basis for the Versatile Interactions of Smad7 with Regulator WW Domains in TGF-beta Pathways.
Authors: Aragon, E. / Goerner, N. / Xi, Q. / Gomes, T. / Gao, S. / Massague, J. / Macias, M.J.
History
DepositionJun 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4-like
B: Smad7 derived peptide


Theoretical massNumber of molelcules
Total (without water)5,7452
Polymers5,7452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300structures with the lowest energy
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4-like / NEDD4.2 / Nedd4-2


Mass: 3966.360 Da / Num. of mol.: 1 / Fragment: WW2 domain (UNP residues 385-417)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: petM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96PU5
#2: Protein/peptide Smad7 derived peptide


Mass: 1778.955 Da / Num. of mol.: 1 / Fragment: UNP residues 203-217 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15105

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HN(CA)CB

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] NEDD4LWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW2-11
2 mMSMAD7-21
20 mMTRIS-3[U-100% 2H]1
100 mMsodium chloride-41
1 mMNEDD4LWW2-5[U-100% 13C; U-100% 15N]2
3 mMSMAD7-62
20 mMTRIS-7[U-100% 2H]2
100 mMsodium chloride-82
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 285 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 30

+
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