cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / cerebral cortex radial glia-guided migration / regulation of nervous system development / positive regulation of neutrophil migration / negative regulation of neuron projection regeneration / endoplasmic reticulum tubular network membrane organization / Axonal growth inhibition (RHOA activation) ...cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / cerebral cortex radial glia-guided migration / regulation of nervous system development / positive regulation of neutrophil migration / negative regulation of neuron projection regeneration / endoplasmic reticulum tubular network membrane organization / Axonal growth inhibition (RHOA activation) / endoplasmic reticulum tubular network membrane / negative regulation of vasculogenesis / : / positive regulation of artery morphogenesis / positive regulation of glial cell differentiation / positive regulation of macrophage migration / : / cell migration involved in vasculogenesis / positive regulation of protein localization to endoplasmic reticulum / intracellular sphingolipid homeostasis / endoplasmic reticulum tubular network / regulation of branching morphogenesis of a nerve / central nervous system vasculogenesis / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of mammary gland epithelial cell proliferation / negative regulation of axonogenesis / nuclear pore complex assembly / regulation of sensory perception of pain / protein localization to lysosome / cardiac epithelial to mesenchymal transition / negative regulation of axon extension / positive regulation of dopamine secretion / leukocyte migration involved in inflammatory response / blastocyst formation / endoplasmic reticulum organization / positive regulation of hepatocyte proliferation / axonal fasciculation / positive regulation of macrophage cytokine production / positive regulation of epithelial cell migration / positive regulation of Rac protein signal transduction / negative regulation of amyloid-beta formation / negative regulation of neuron differentiation / regulation of cell migration / cell projection / negative regulation of cell growth / positive regulation of angiogenesis / nuclear envelope / cell junction / negative regulation of neuron projection development / myelin sheath / cellular response to hypoxia / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / protein stabilization / cadherin binding / neuron projection / neuronal cell body / ubiquitin protein ligase binding / glutamatergic synapse / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2480 / Reticulon / Reticulon / Reticulon domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Method: simulated annealing / Software ordinal: 1 Details: XPLOR-NIH WAS USED FOR REFINING THE FOLDED PROTEINS. DIHERAL ANGLE RESTRAINTS AND PRE RESTRAINTS WERE ADDED DURING REFINEMENT.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 10
+
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