[English] 日本語
Yorodumi
- PDB-1f2h: SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE TNFR1 ASSOCIAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f2h
TitleSOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE TNFR1 ASSOCIATED PROTEIN, TRADD.
ComponentsTUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN
KeywordsAPOPTOSIS / TNFR-1 associated protein
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex ...tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / tumor necrosis factor receptor binding / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / kinase binding / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / cytoskeleton / receptor complex / positive regulation of cell migration / positive regulation of apoptotic process / apoptotic process / protein-containing complex binding / signal transduction / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TRADD, N-terminal domain / TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily ...TRADD, N-terminal domain / TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing
Model type detailsminimized average
AuthorsTsao, D. / McDonaugh, T. / Malakian, K. / Xu, G.-Y. / Telliez, J.-B. / Hsu, H. / Lin, L.-L.
CitationJournal: Mol.Cell / Year: 2000
Title: Solution structure of N-TRADD and characterization of the interaction of N-TRADD and C-TRAF2, a key step in the TNFR1 signaling pathway.
Authors: Tsao, D.H. / McDonagh, T. / Telliez, J.B. / Hsu, S. / Malakian, K. / Xu, G.Y. / Lin, L.L.
History
DepositionMay 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
A: TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,5721
Polymers18,5721
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)1 / 1Low energies and violations not larger than 0.3A for NOEs and 5 degrees for torsional restraints
Representativeminimized average structure

-
Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN / TRADD / TNFR1-ASSOCIATED DEATH DOMAIN PROTEIN


Mass: 18572.160 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSETB / Production host: Escherichia coli (E. coli) / References: UniProt: Q15628

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
241HN(CA)CB
251HN(CO)CACB
261C(CO)NH-TOCSY
371hcchtocsy
281HAHB(CO)NH
19115N-edited TOCSY-HSQC
3101methyl-methyl NOE
NMR detailsText: Other experiments used were HC(CO)NH_TOCSY, 3D 13C-13C long range correlation, methyl-methyl NOE

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM 15N N-TRADD20mM Imidazole pH 6.6 200 mMNaCL 20 mM DTT 0.05%NaN3 90%H2O 10% D2O
21.1 mM 15N/13C N-TRADD20mM Imidazole pH 6.6 200 mMNaCL 20 mM DTT 0.05%NaN3 90%H2O 10% D2O
30.8 mM 15N/13C N-TRADD20mM Imidazole pH 6.6 200 mMNaCL 220 mM DTT 0.05%NaN3 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200mM NaCl 6.6 1 atm298 K
2200mM NaCl 6.6 1 atm298 K
3200mM NaCl 6.6 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger et al / Classification: refinement
RefinementMethod: Distance geometry, simulated annealing / Software ordinal: 1
Details: Structures determined from 2402 restraints (1883 NOE restraints, 159 dihedral, 100 distance restraints from hydrogen bonds and 240 Alpha and Beta 13C chemical shifts).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: Low energies and violations not larger than 0.3A for NOEs and 5 degrees for torsional restraints
Conformers calculated total number: 1 / Conformers submitted total number: 1

+
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://pdbjlvh1.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