[English] 日本語
Yorodumi
- PDB-1i5h: SOLUTION STRUCTURE OF THE RNEDD4 WWIII DOMAIN-RENAL BP2 PEPTIDE C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i5h
TitleSOLUTION STRUCTURE OF THE RNEDD4 WWIII DOMAIN-RENAL BP2 PEPTIDE COMPLEX
Components
  • AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT
  • UBIQUITIN LIGASE NEDD4
KeywordsLIGASE / Nedd4 / WW domains / ENaC / PY Motif / Liddle syndrome / proline-rich
Function / homology
Function and homology information


Sensory perception of salty taste / Downregulation of ERBB4 signaling / Regulation of PTEN localization / Stimuli-sensing channels / sensory perception of salty taste / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / neutrophil-mediated killing of bacterium ...Sensory perception of salty taste / Downregulation of ERBB4 signaling / Regulation of PTEN localization / Stimuli-sensing channels / sensory perception of salty taste / ISG15 antiviral mechanism / positive regulation of nucleocytoplasmic transport / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / neutrophil-mediated killing of bacterium / aldosterone metabolic process / leukocyte activation involved in inflammatory response / cellular response to vasopressin / sensory perception of sour taste / negative regulation of sodium ion transport / cellular response to aldosterone / channel inhibitor activity / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of body fluid levels / response to denervation involved in regulation of muscle adaptation / endocardial cushion development / sodium channel complex / negative regulation of potassium ion export across plasma membrane / epithelial fluid transport / mucus secretion / sodium ion homeostasis / renal system process / regulation protein catabolic process at postsynapse / neutrophil activation involved in immune response / artery smooth muscle contraction / phosphothreonine residue binding / multicellular organismal-level water homeostasis / receptor catabolic process / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein targeting to lysosome / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / potassium ion homeostasis / HECT-type E3 ubiquitin transferase / intracellular sodium ion homeostasis / proline-rich region binding / potassium channel inhibitor activity / sodium channel inhibitor activity / blood vessel morphogenesis / RNA polymerase binding / sodium ion import across plasma membrane / wound healing, spreading of epidermal cells / beta-2 adrenergic receptor binding / lysosomal transport / negative regulation of vascular endothelial growth factor receptor signaling pathway / lung alveolus development / blood circulation / ligand-gated sodium channel activity / WW domain binding / regulation of postsynaptic neurotransmitter receptor internalization / erythrocyte homeostasis / regulation of dendrite morphogenesis / response to food / sodium channel activity / neuromuscular junction development / regulation of synapse organization / sodium ion transport / microvillus / progesterone receptor signaling pathway / outflow tract morphogenesis / phosphoserine residue binding / protein monoubiquitination / protein K63-linked ubiquitination / ubiquitin ligase complex / postsynaptic cytosol / regulation of sodium ion transport / cellular response to acidic pH / establishment of localization in cell / ionotropic glutamate receptor binding / cytoplasmic vesicle membrane / T cell activation / sodium ion transmembrane transport / ubiquitin binding / regulation of membrane potential / receptor internalization / regulation of blood pressure / multicellular organism growth / neuron projection development / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / cellular response to UV / ubiquitin protein ligase activity / cell cortex / transcription by RNA polymerase II / gene expression / ubiquitin-dependent protein catabolic process / adaptive immune response / transmembrane transporter binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / apical plasma membrane / immune response / protein ubiquitination / response to xenobiotic stimulus / inflammatory response / external side of plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / : / HECT domain ...Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / 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 / Single Sheet / C2 domain superfamily / Mainly Beta
Similarity search - Domain/homology
Epithelial sodium channel subunit beta / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKanelis, V. / Rotin, D. / Forman-Kay, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Solution structure of a Nedd4 WW domain-ENaC peptide complex.
Authors: Kanelis, V. / Rotin, D. / Forman-Kay, J.D.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
W: UBIQUITIN LIGASE NEDD4
B: AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT


Theoretical massNumber of molelcules
Total (without water)7,3922
Polymers7,3922
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)15 / 170structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide UBIQUITIN LIGASE NEDD4 / RNEDD4


Mass: 5666.237 Da / Num. of mol.: 1 / Fragment: WWIII DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62940
#2: Protein/peptide AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT / RENAL BP2 PEPTIDE


Mass: 1725.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: AN IDENTICAL PEPTIDE WAS MADE SYNTHETICALLY USING STANDARD F-MOC CHEMISTRY FOR NMR SAMPLES REQUIRING UNLABELED BP2 PEPTIDE.
Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37090

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N/13C-edited NOESY
1233D 13C F1-filtered, F3-edited NOESY
1323D 15N/13C-edited NOESY
1443D 13C F1-filtered, F3-edited NOESY
152HN(CO)CA COHACA CROSS
162HN(CO)CA HNHA CROSS
171J-HNHA
182J-HNHA
191HNCO-TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1Sample 1:1mM rNedd4 WWIII U-15N,13C; 3mM rENaC bP2 NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF; Sample 2:1mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF; MORE DETAILED DESCRIPTION GIVEN IN BMRB 496390% H2O/10% D2O
21mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;90% H2O/10% D2O
31mM rNedd4 WWIII U-15N,13C; 3mM rENaC bP2 NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;100% D2O
41mM rENaC bP2 U-15N,13C; 3mM rNedd4 WWIII NA; 10 mM Na+ phosphate, pH 6.5; 0.005 mM EDTA; 0.01 mM aprotinin; 0.005 mM leupeptin; 0.005 mM AEBSF;100% D2O
Sample conditionsIonic strength: 0.01 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A.processing
NMRVeiw4.1.2Johnson, B.A and Blevis, B.A.data analysis
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and warren, G.L.structure solution
ARIA1Nilges, M.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Preliminary structures were calculated using CNS1.0. These structures were then used as input into the program ARIA1.0 for noe assignment and structure refinement. These structures were ...Details: Preliminary structures were calculated using CNS1.0. These structures were then used as input into the program ARIA1.0 for noe assignment and structure refinement. These structures were calculated using 1799 unambiguous and 214 ambiguous NOEs, 14 hydrogen bond restraints, 44 dihedral angle restraints and directly refined against 33 Jhnha coupling constants.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 170 / Conformers submitted total number: 15

+
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