[English] 日本語
Yorodumi
- PDB-1ngr: DEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ngr
TitleDEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES 334-418, NMR, 20 STRUCTURES
ComponentsP75 LOW AFFINITY NEUROTROPHIN RECEPTOR
KeywordsRECEPTOR / P75 / INTRACELLULAR DOMAIN / NEUROTROPHIN RECEPTOR / DEATH DOMAIN
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / death receptor activity / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / positive regulation of synaptic transmission, cholinergic / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / negative regulation of dendritic spine development / positive regulation of myelination / nerve development / clathrin-coated endocytic vesicle / nerve growth factor binding / neurotrophin TRKA receptor binding / positive regulation of neural precursor cell proliferation / regulation of reactive oxygen species metabolic process / negative regulation of mitochondrial depolarization / skin development / hair follicle morphogenesis / positive regulation of Rho protein signal transduction / neuronal cell body membrane / skeletal muscle cell differentiation / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / positive regulation of excitatory postsynaptic potential / Rho protein signal transduction / hair follicle development / fibroblast growth factor receptor signaling pathway / coreceptor activity / dendrite membrane / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / negative regulation of angiogenesis / positive regulation of synaptic transmission, glutamatergic / negative regulation of cell migration / central nervous system development / positive regulation of apoptotic signaling pathway / axon guidance / intracellular protein transport / circadian regulation of gene expression / neuromuscular junction / small GTPase binding / positive regulation of neuron projection development / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / positive regulation of fibroblast proliferation / cell-cell junction / presynapse / negative regulation of neuron projection development / glucose homeostasis / presynaptic membrane / nuclear envelope / cellular response to oxidative stress / amyloid-beta binding / growth cone / fibroblast proliferation / regulation of gene expression / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / dendritic spine / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / calmodulin binding / positive regulation of apoptotic process / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. ...Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / VARIABLE TARGET FUNCTION (DIANA) APPROACH
AuthorsOtting, G. / Liepinsh, E.
CitationJournal: EMBO J. / Year: 1997
Title: NMR structure of the death domain of the p75 neurotrophin receptor.
Authors: Liepinsh, E. / Ilag, L.L. / Otting, G. / Ibanez, C.F.
History
DepositionJan 28, 1997Processing site: BNL
Revision 1.0Jul 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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
A: P75 LOW AFFINITY NEUROTROPHIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)9,4301
Polymers9,4301
Non-polymers00
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 / 50LOWEST TARGET FUNCTION AFTER DIANA
Representative

-
Components

#1: Protein P75 LOW AFFINITY NEUROTROPHIN RECEPTOR


Mass: 9429.558 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN, RESIDUES 281 - 425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: NERVE CELLS / Cellular location: CYTOPLASM / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15-(PREP4) / References: UniProt: P07174

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
1413D NOESY-15N-HSQC
1513D TOCSY-HSQC
1613D HNHA
NMR detailsText: DISTANCE CONSTRAINTS FROM 3D NOESY-15N-HSQC AND 2D NOESY, COUPLING CONSTANTS FROM 3D HNHA-EXPERIMENT, 2QF-COSY, AND 15N-HSQC. A 15N-LABELED SAMPLE OF P75ICD WAS USED. CONSTRAINTS USED: 914 ...Text: DISTANCE CONSTRAINTS FROM 3D NOESY-15N-HSQC AND 2D NOESY, COUPLING CONSTANTS FROM 3D HNHA-EXPERIMENT, 2QF-COSY, AND 15N-HSQC. A 15N-LABELED SAMPLE OF P75ICD WAS USED. CONSTRAINTS USED: 914 UPPER DISTANCE LIMITS FROM NOE DATA 154 COUPLING CONSTANTS CONSTRAINING DIHEDRAL ANGLES IONIC_STRENGTH: NO SALT ADDED PRESSURE: 1 ATM SOLVENT SYSTEM: 90% H2O/10% D2O

-
Sample preparation

Sample conditionspH: 7.0 / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX800BrukerDMX8008001
Bruker DMX600BrukerDMX6006002

-
Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHLrefinement
EASYstructure solution
HABASstructure solution
DIANAstructure solution
OPALstructure solution
RefinementMethod: VARIABLE TARGET FUNCTION (DIANA) APPROACH / Software ordinal: 1
Details: DIANA MINIMIZATION TO TARGET FUNCTION LESS THAN 1, RESTRAINED ENERGY MINIMIZATION USING OPAL
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION AFTER DIANA
Conformers calculated total number: 50 / 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