[English] 日本語
Yorodumi
- PDB-1ujd: Solution Structure of RSGI RUH-003, a PDZ domain of hypothetical ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ujd
TitleSolution Structure of RSGI RUH-003, a PDZ domain of hypothetical KIAA0559 protein from human cDNA
ComponentsKIAA0559 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / human cdna / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / profilin binding / protein localization to synapse / regulation of exocytosis / calcium-dependent phospholipid binding / insulin secretion / synaptic vesicle exocytosis ...presynaptic active zone assembly / presynapse to nucleus signaling pathway / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / profilin binding / protein localization to synapse / regulation of exocytosis / calcium-dependent phospholipid binding / insulin secretion / synaptic vesicle exocytosis / cAMP-mediated signaling / GABA-ergic synapse / cytoskeleton organization / postsynaptic density / cytoskeleton / axon / glutamatergic synapse / synapse / calcium ion binding / extracellular exosome
Similarity search - Function
Zinc finger, piccolo-type / Protein piccolo / Piccolo, FYVE-related domain 1 / Piccolo Zn-finger / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PDZ domain / Pdz3 Domain ...Zinc finger, piccolo-type / Protein piccolo / Piccolo, FYVE-related domain 1 / Piccolo Zn-finger / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PDZ domain / Pdz3 Domain / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsOhashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution Structure of RSGI RUH-003, a PDZ domain of hypothetical KIAA0559 protein from human cDNA
Authors: Ohashi, W. / Hirota, H. / Yamazaki, T. / Muto, Y. / Yokoyama, S.
History
DepositionJul 31, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KIAA0559 protein


Theoretical massNumber of molelcules
Total (without water)12,2801
Polymers12,2801
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 / 100The submitted conformer models are those with the lowest number of target function
RepresentativeModel #1lowest target function

-
Components

#1: Protein KIAA0559 protein


Mass: 12279.770 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 / References: UniProt: Q9Y6V0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

DetailsContents: 1.5mM RSGI RUH-003 U-13C,15N; 20mM Tris-HCl, 100mM NaCl, 1mM DTT U-2H, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe2.1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CYANA1.0.7Guentertstructure solution
CYANA1.0.7Guentertrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: The submitted conformer models are those with the lowest number of 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.

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