[English] 日本語
Yorodumi
- PDB-2i2y: Solution structure of the RRM of SRp20 bound to the RNA CAUC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i2y
TitleSolution structure of the RRM of SRp20 bound to the RNA CAUC
Components
  • (5'-R(*CP*AP*UP*C)-3')
  • Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3
KeywordsRNA binding protein/Chimera/RNA / PROTEIN-RNA COMPLEX RRM alpha-beta sandwich beta1-alpha1-beta2-beta3-alpha2-beta4 / RNA binding protein-Chimera-RNA COMPLEX
Function / homology
Function and homology information


protein-RNA sequence-specific adaptor activity / primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / phospholipase binding / Processing of Capped Intron-Containing Pre-mRNA ...protein-RNA sequence-specific adaptor activity / primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / phospholipase binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA export from nucleus / mRNA Splicing - Major Pathway / cellular response to leukemia inhibitory factor / mRNA splicing, via spliceosome / nuclear speck / RNA binding / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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 / Ubiquitin-like (UB roll) / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Immunoglobulin G-binding protein G / Serine/arginine-rich splicing factor 3
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / AMBER 7
AuthorsHargous, Y.F. / Allain, F.H.
CitationJournal: Embo J. / Year: 2006
Title: Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8.
Authors: Hargous, Y. / Hautbergue, G.M. / Tintaru, A.M. / Skrisovska, L. / Golovanov, A.P. / Stevenin, J. / Lian, L.Y. / Wilson, S.A. / Allain, F.H.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_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 / _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
B: (5'-R(*CP*AP*UP*C)-3')
A: Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3


Theoretical massNumber of molelcules
Total (without water)18,0612
Polymers18,0612
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)28 / 50structures with the least restraint violations
Representative

-
Components

#1: RNA chain (5'-R(*CP*AP*UP*C)-3')


Mass: 1200.778 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: core sequence of exonic splicing enhancers recognised by SRp20
#2: Antibody Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3 / Pre-mRNA-splicing factor SRP20


Mass: 16860.682 Da / Num. of mol.: 1 / Fragment: RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G', Homo sapiens
Genus: Streptococcus, Homo / Species: , / Strain: , / Gene: spg and SFRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+ RIL / References: UniProt: P19909, UniProt: P84103

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CBCA(CO)NH
1313D 13C-separated NOESY
1423D 15N-separated NOESY
151(H)CCH TOCSY
1622D NOESY
1722D TOCSY
1833D flitered [1H,13C,1H] NOESY
1912D filtered/edited NOESY
1101

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM SRp20 13C-15N labelled + 1 mM CAUC natural abundance in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O,90% H2O or 100% D2O
21mM SRp20 15N labelled + 1 mM CAUC natural abundance in 1mM SRp20 15N labelled in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT10% D2O, 90% H2O or 100% D2O
31mM SRp20 15N labelled + 1 mM CAUC with 13C labelled riboses and natural abundance bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
41mM SRp20 15N labelled + 1 mM CAUC with A2 and U3 riboses 13C labelled and natural abundance of other riboses and all bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
51mM SRp20 15N labelled + 1 mM CAUC with C1 and C4 riboses 13C labelled and natural abundance of other riboses and all bases, in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 315 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX9001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX6003

-
Processing

NMR software
NameDeveloperClassification
DIANAstructure solution
Sparkydata analysis
Amber 7Case and Cornellrefinement
RefinementMethod: AMBER 7 / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 28

+
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