[English] 日本語
Yorodumi
- PDB-2lec: Solution structure of human SRSF2 (SC35) RRM in complex with 5'-U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lec
TitleSolution structure of human SRSF2 (SC35) RRM in complex with 5'-UGGAGU-3'
Components
  • RNA (5'-R(*UP*GP*GP*AP*GP*U)-3')
  • Serine/arginine-rich splicing factor 2
KeywordsRNA binding protein/RNA / SR protein / splicing factor / RNA protein complex / RNA binding protein-RNA complex
Function / homology
Function and homology information


interchromatin granule / perichromatin fibrils / pre-mRNA binding / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / response to vitamin E ...interchromatin granule / perichromatin fibrils / pre-mRNA binding / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / response to vitamin E / mRNA Splicing - Major Pathway / protein kinase C binding / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear speck / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
RNA recognition motif domain, eukaryote / RNA recognition motif / 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 ...RNA recognition motif domain, eukaryote / RNA recognition motif / 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 / Serine/arginine-rich splicing factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 14
AuthorsDaubner, G.M. / Clery, A. / Jayne, S. / Stevenin, J. / Allain, F.H.-T.
CitationJournal: Embo J. / Year: 2012
Title: A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well.
Authors: Daubner, G.M. / Clery, A. / Jayne, S. / Stevenin, J. / Allain, F.H.
History
DepositionJun 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/arginine-rich splicing factor 2
B: RNA (5'-R(*UP*GP*GP*AP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
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 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Serine/arginine-rich splicing factor 2 / Protein PR264 / Splicing component / 35 kDa / Splicing factor SC35 / SC-35 / Splicing factor / ...Protein PR264 / Splicing component / 35 kDa / Splicing factor SC35 / SC-35 / Splicing factor / arginine/serine-rich 2


Mass: 15258.074 Da / Num. of mol.: 1 / Fragment: RRM domain residues 1-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFRS2, SRSF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01130
#2: RNA chain RNA (5'-R(*UP*GP*GP*AP*GP*U)-3')


Mass: 1932.197 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
1212D 1H-13C HSQC
1313D HCACO
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11213D 1H-13C NOESY
11313D 1H-15N NOESY
11422D 1H-1H NOESY
11522D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-15N] SRSF2 RRM + UGGAGU1, 0.75 mM [U-13C; U-15N] SRSF2 RRM + UGGAGU2, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-15N] SRSF2 RRM + UGGAGU1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMSRSF2 RRM + UGGAGU1-1[U-15N]1
0.75 mMSRSF2 RRM + UGGAGU2-2[U-13C; U-15N]1
0.75 mMSRSF2 RRM + UGGAGU1-3[U-15N]2
Sample conditionsIonic strength: 120 / pH: 5.5 / Pressure: ambient / Temperature: 310.8 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance6002
Bruker AvanceBrukerAvance7003
Bruker AvanceBrukerAvance9004

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AMBER9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
SPARKYGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2181 / NOE intraresidue total count: 486 / NOE long range total count: 673 / NOE medium range total count: 396 / NOE sequential total count: 626
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.3 Å

+
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