[English] 日本語
Yorodumi
- PDB-5x3y: Refined solution structure of musashi1 RBD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x3y
TitleRefined solution structure of musashi1 RBD2
ComponentsRNA-binding protein Musashi homolog 1
KeywordsRNA BINDING PROTEIN / RNA-binding protein / RRM / RBD
Function / homology
Function and homology information


poly(U) RNA binding / epithelial cell differentiation / response to hormone / central nervous system development / regulation of translation / single-stranded RNA binding / mRNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA-binding protein Musashi homologue, RNA recognition motif 2 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / 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
RNA-binding protein Musashi homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsIwaoka, R. / Nagata, T. / Tsuda, K. / Imai, T. / Okano, H. / Kobayashi, N. / Katahira, M.
Funding support Japan, 5items
OrganizationGrant numberCountry
JSPS15H01256 Japan
JSPS16H00833 Japan
JSPS16K14678 Japan
JSPS15H01634 Japan
JSPS26440026 Japan
CitationJournal: Molecules / Year: 2017
Title: Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA
Authors: Iwaoka, R. / Nagata, T. / Tsuda, K. / Imai, T. / Okano, H. / Kobayashi, N. / Katahira, M.
History
DepositionFeb 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein Musashi homolog 1


Theoretical massNumber of molelcules
Total (without water)10,9461
Polymers10,9461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7390 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein RNA-binding protein Musashi homolog 1 / Musashi-1


Mass: 10945.506 Da / Num. of mol.: 1 / Fragment: UNP residues 109-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msi1, Msi1h / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q61474

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
133isotropic13D 1H-15N NOESY
143isotropic13D 1H-13C NOESY
153isotropic13D HNCO
163isotropic13D CBCA(CO)NH
173isotropic13D HN(CA)CB
183isotropic13D HNCA
193isotropic13D HBHA(CO)NH
1103isotropic13D (H)CCH-TOCSY
1113isotropic13D (H)CCH-COSY

-
Sample preparation

DetailsType: solution
Contents: 250 uM [U-100% 13C; U-100% 15N] Msi1 RBD2, 95% H2O/5% D2O
Label: 15N/13C_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 250 uM / Component: Msi1 RBD2 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.0 / Pressure: ambient atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGROKobayashichemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / 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://pdbjlvh1.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