[English] 日本語
Yorodumi
- PDB-2dbh: Solution structure of the carboxyl-terminal CARD-like domain in h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dbh
TitleSolution structure of the carboxyl-terminal CARD-like domain in human TNFR-related death receptor-6
ComponentsTumor necrosis factor receptor superfamily member 21
KeywordsSIGNALING PROTEIN / Apoptosis / TNF RECEPTOR SUPERFAMILY / NF-kappaB / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of oligodendrocyte differentiation / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of myelination / B cell apoptotic process / axonal fasciculation / oligodendrocyte apoptotic process / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / humoral immune response ...regulation of oligodendrocyte differentiation / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of myelination / B cell apoptotic process / axonal fasciculation / oligodendrocyte apoptotic process / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / humoral immune response / negative regulation of T cell proliferation / myelination / PPARA activates gene expression / cellular response to tumor necrosis factor / T cell receptor signaling pathway / neuron apoptotic process / adaptive immune response / axon / apoptotic process / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death 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 ...Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death 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 / Putative ephrin-receptor like / 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 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Inoue, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the carboxyl-terminal CARD-like domain in human TNFR-related death receptor-6
Authors: Saito, K. / Inoue, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Tumor necrosis factor receptor superfamily member 21


Theoretical massNumber of molelcules
Total (without water)11,2141
Polymers11,2141
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Tumor necrosis factor receptor superfamily member 21 / DR6 / TNFR-related death receptor 6 / Death receptor 6


Mass: 11213.504 Da / Num. of mol.: 1 / Fragment: CARD-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: AB2445_D11 / Plasmid: P050801-03 / References: UniProt: O75509

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

-
Sample preparation

DetailsContents: 1mM protein, 20mM d-tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
NMRPipe2002DELAGLIO, F.processing
NIRVIEW5JOHNSON,BAdata analysis
CNS1.1BRUNGER ATstructure solution
CNS1.1BRUNGER ATrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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