- PDB-2yuc: Solution structure of the TRAF-type zinc finger domains (102-164)... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2yuc
Title
Solution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4
Components
TNF receptor-associated factor 4
Keywords
SIGNALING PROTEIN / zf-TRAF / Cysteine-rich domain associated with RING and Traf domains protein 1 / Malignant 62 / RING finger protein 83 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information
respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / bicellular tight junction / positive regulation of protein kinase activity / tumor necrosis factor-mediated signaling pathway ...respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / bicellular tight junction / positive regulation of protein kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / fibrillar center / transferase activity / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / innate immune response / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function
Method: torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 918 restraints, 870 are NOE-derived distance constraints, 48 dihedral angle restraints.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the least restraint violations, target function 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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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