[English] 日本語
Yorodumi
- PDB-2n8t: Solution Structure of the rNedd4 WW2 Domain-Cx43CT Peptide Comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n8t
TitleSolution Structure of the rNedd4 WW2 Domain-Cx43CT Peptide Complex by NMR
Components
  • Cx43CT Peptide
  • E3 ubiquitin-protein ligase NEDD4
KeywordsLIGASE/peptide / rNedd4 WW2 / Cx43CT / phosphorylation / LIGASE / LIGASE-peptide complex
Function / homology
Function and homology information


vascular transport / positive regulation of striated muscle tissue development / milk ejection reflex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / atrial ventricular junction remodeling / positive regulation of cell communication by chemical coupling / Gap junction assembly / cell communication by chemical coupling / Downregulation of ERBB4 signaling ...vascular transport / positive regulation of striated muscle tissue development / milk ejection reflex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Regulation of gap junction activity / atrial ventricular junction remodeling / positive regulation of cell communication by chemical coupling / Gap junction assembly / cell communication by chemical coupling / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ISG15 antiviral mechanism / epididymis development / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / positive regulation of glomerular filtration / RHOQ GTPase cycle / Antigen processing: Ubiquitination & Proteasome degradation / neuroblast migration / columnar/cuboidal epithelial cell maturation / negative regulation of gonadotropin secretion / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / positive regulation of behavioral fear response / cell communication by electrical coupling / positive regulation of smooth muscle cell chemotaxis / regulation of bone remodeling / chronic inflammatory response / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of DNA biosynthetic process / maintenance of protein localization in endoplasmic reticulum / contractile muscle fiber / Gap junction degradation / Formation of annular gap junctions / negative regulation of sodium ion transport / regulation of cell communication by electrical coupling / nuclear receptor-mediated glucocorticoid signaling pathway / ATP transport / negative regulation of trophoblast cell migration / response to denervation involved in regulation of muscle adaptation / microtubule-based transport / gap junction channel activity involved in cell communication by electrical coupling / endocardial cushion development / gap junction hemi-channel activity / monoatomic ion transmembrane transporter activity / positive regulation of meiotic nuclear division / positive regulation of establishment of Sertoli cell barrier / endothelium development / negative regulation of cardiac muscle cell proliferation / gap junction assembly / cellular response to pH / regulation of atrial cardiac muscle cell membrane depolarization / fascia adherens / regulation protein catabolic process at postsynapse / glutathione transmembrane transporter activity / cardiac conduction / regulation of actin filament organization / connexin complex / receptor catabolic process / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell contact zone / phosphothreonine residue binding / gap junction / protein targeting to lysosome / Golgi-associated vesicle membrane / response to fluid shear stress / skeletal muscle tissue regeneration / regulation of monoatomic ion transmembrane transport / regulation of bone mineralization / regulation of transmembrane transporter activity / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / gap junction channel activity / bone remodeling / connexin binding / regulation of ventricular cardiac muscle cell membrane repolarization / adult heart development / HECT-type E3 ubiquitin transferase / export across plasma membrane / cell-cell junction organization / embryonic heart tube development / sodium channel inhibitor activity / proline-rich region binding / response to pH / RNA polymerase binding / glutamate secretion / blood vessel morphogenesis / lens development in camera-type eye / intermediate filament / beta-2 adrenergic receptor binding / tight junction / lysosomal transport / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / embryonic digit morphogenesis / xenobiotic transport / regulation of dendrite morphogenesis / negative regulation of vascular endothelial growth factor receptor signaling pathway / sodium ion transport / regulation of postsynaptic neurotransmitter receptor internalization / neuromuscular junction development
Similarity search - Function
Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / E3 ubiquitin-protein ligase, SMURF1 type / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain ...Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / E3 ubiquitin-protein ligase, SMURF1 type / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain / : / 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 / C2 domain / C2 domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
Gap junction alpha-1 protein / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsSpagnol, G. / Kieken, F. / Sorgen, P.L.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Studies of the Nedd4 WW Domains and Their Selectivity for the Connexin43 (Cx43) Carboxyl Terminus.
Authors: Spagnol, G. / Kieken, F. / Kopanic, J.L. / Li, H. / Zach, S. / Stauch, K.L. / Grosely, R. / Sorgen, P.L.
History
DepositionOct 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4
B: Cx43CT Peptide


Theoretical massNumber of molelcules
Total (without water)6,0532
Polymers6,0532
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4


Mass: 4435.713 Da / Num. of mol.: 1 / Fragment: WW2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nedd4, Nedd4a / Production host: Escherichia coli (E. coli)
References: UniProt: Q62940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Cx43CT Peptide / Connexin-43 / Cx43 / Gap junction 43 kDa heart protein


Mass: 1617.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized, purchased from a vendor / References: UniProt: P08050
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNHA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 0.6 mM [U-98% 13C; U-98% 15N] rNedd4 WW2, 13 mM Cx43CT peptide, 1.8 mM potassium phosphate, 1 mM DTT, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMrNedd4 WW2-1[U-98% 13C; U-98% 15N]1
13 mMCx43CT peptide-21
1.8 mMpotassium phosphate-31
1 mMDTT-41
137 mMsodium chloride-51
2.7 mMpotassium chloride-61
10 mMsodium phosphate-71
Sample conditionsIonic strength: 156 / pH: 7.5 / Pressure: ambient / Temperature: 25 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Dr. Michael Nilges, Institut Pasteurrefinement
ARIA1.1Dr. Michael Nilges, Institut Pasteurgeometry optimization
ARIA1.1Dr. Michael Nilges, Institut Pasteurstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
NMRDrawF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

+
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