[English] 日本語
Yorodumi
- PDB-2ru3: Solution structure of c.elegans SUP-12 RRM in complex with RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ru3
TitleSolution structure of c.elegans SUP-12 RRM in complex with RNA
Components
  • Protein SUP-12, isoform a
  • RNA (5'-R(*GP*UP*GP*UP*GP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / solution structure / Protein-RNA Complex / RRM (RNA recognition motif) / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / pre-mRNA binding / regulation of locomotion / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / regulation of actin cytoskeleton organization / single-stranded RNA binding / nuclear speck / ribonucleoprotein complex
Similarity search - Function
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 / RRM domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsTakahashi, M. / Kuwasako, K. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. ...Takahashi, M. / Kuwasako, K. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. / Tanaka, A. / Yokoyama, S. / Hagiwara, M. / Kuroyanagi, H. / Muto, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Authors: Kuwasako, K. / Takahashi, M. / Unzai, S. / Tsuda, K. / Yoshikawa, S. / He, F. / Kobayashi, N. / Guntert, P. / Shirouzu, M. / Ito, T. / Tanaka, A. / Yokoyama, S. / Hagiwara, M. / Kuroyanagi, H. / Muto, Y.
History
DepositionNov 12, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SUP-12, isoform a
B: RNA (5'-R(*GP*UP*GP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)13,3352
Polymers13,3352
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Protein SUP-12, isoform a


Mass: 11426.773 Da / Num. of mol.: 1 / Fragment: RNA recognition motif (RRM), UNP residues 20-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sup-12, CELE_T22B2.4, T22B2.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O45189
#2: RNA chain RNA (5'-R(*GP*UP*GP*UP*GP*C)-3')


Mass: 1908.173 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1612D 1H-13C HSQC
1713D HBHA(CO)NH
1813D C(CO)NH
1913D H(CCO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11212D 1H-1H NOESY

-
Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] SUP-12-1, 0.72 mM RNA-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMSUP-12-1[U-100% 13C; U-100% 15N]1
0.72 mMRNA-21
Sample conditionsIonic strength: 0.1 / pH: 5-7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR softwareName: Amber / Version: 9
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

+
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