[English] 日本語
Yorodumi
- PDB-2dnr: Solution structure of RNA binding domain in Synaptojanin 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dnr
TitleSolution structure of RNA binding domain in Synaptojanin 1
ComponentsSynaptojanin-1
KeywordsRNA BINDING PROTEIN / RRM domain / RBD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / clathrin coat of coated pit ...positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / clathrin coat of coated pit / synaptic vesicle uncoating / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol dephosphorylation / membrane coat / membrane organization / phosphatidylinositol biosynthetic process / vesicle membrane / neurotransmitter transport / synaptic vesicle priming / synaptic vesicle transport / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / synaptic vesicle endocytosis / learning / synaptic membrane / terminal bouton / SH3 domain binding / Clathrin-mediated endocytosis / presynapse / perinuclear region of cytoplasm / RNA binding / cytosol
Similarity search - Function
Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 ...Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Endonuclease/exonuclease/phosphatase superfamily / RRM (RNA recognition motif) domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RNA binding domain in Synaptojanin 1
Authors: Tsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptojanin-1


Theoretical massNumber of molelcules
Total (without water)9,6561
Polymers9,6561
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)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Synaptojanin-1 / Synaptic inositol-1 / 4 / 5-trisphosphate 5- phosphatase 1


Mass: 9655.860 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ1 / Plasmid: P050725-04 / Production host: Cell free synthesis / References: UniProt: O43426, phosphoinositide 5-phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

-
Sample preparation

DetailsContents: 1.11mM 13C-15N PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio,Fprocessing
NMRView5.0.4Johnson,B.Adata analysis
KUJIRA0.9742Kobayashi,Ndata analysis
CYANA2.0.17Guntert,Pstructure solution
CYANA2.0.17Guntert,Prefinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
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