|Entry||Database: PDB / ID: 1um1|
|Title||Solution Structure of RSGI RUH-007, PDZ domain in Human cDNA|
|Keywords||STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / Human cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI|
|Function / homology|
Function and homology information
substrate adhesion-dependent cell spreading / microtubule / multicellular organism development / signal transduction / protein-containing complex
Ubiquitin-like domain superfamily / PDZ superfamily / PDZ domain / Rasip1/Radil, cargo-binding domain / Ras-associating (RA) domain / PDZ domain / Dilute domain / SMAD/FHA domain superfamily / PDZ domain / Pdz3 Domain ...Ubiquitin-like domain superfamily / PDZ superfamily / PDZ domain / Rasip1/Radil, cargo-binding domain / Ras-associating (RA) domain / PDZ domain / Dilute domain / SMAD/FHA domain superfamily / PDZ domain / Pdz3 Domain / Roll / Mainly Beta
Ras-associating and dilute domain-containing protein
|Biological species||Homo sapiens (human)|
|Method||SOLUTION NMR / torsion angle dynamics|
|Authors||Doi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)|
|Citation||Journal: To be Published|
Title: Solution Structure of RSGI RUH-007, a PDZ Domain in Human cDNA
Authors: Doi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: KIAA1849 protein
|#1: Protein|| |
Mass: 11302.925 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA KIAA1849 / Plasmid: P021030-50 / References: UniProt: Q96JH8
|Experiment||Method: SOLUTION NMR|
|Details||Contents: 0.7mM PDZ domain U-15N, 13C; 20mM Tris-HCl (pH 7.0); 100mM NaCl; 0.02% NaN3; 90% H2O, 10% D2O|
Solvent system: 90% H2O/10% D2O
|Sample conditions||Ionic strength: 120mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M|
|Radiation wavelength||Relative weight: 1|
|NMR spectrometer||Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz|
|Refinement||Method: torsion angle dynamics / Software ordinal: 1|
|NMR representative||Selection criteria: lowest energy|
|NMR ensemble||Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function|
Conformers calculated total number: 100 / Conformers submitted total number: 20
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- 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.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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