[English] 日本語
Yorodumi
- PDB-2xeb: NMR STRUCTURE OF THE PROTEIN-UNBOUND SPLICEOSOMAL U4 SNRNA 5' STE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xeb
TitleNMR STRUCTURE OF THE PROTEIN-UNBOUND SPLICEOSOMAL U4 SNRNA 5' STEM LOOP
Components
  • 5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP* GP*GP*UP*U)-3'
  • 5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3'
KeywordsRNA / PRE-MRNA SPLICING / U4/U6 DI-SNRNP / RNP-BINDING DOMAIN / SANS
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / RDC REFINEMENT, WATER REFINEMENT
AuthorsFalb, M. / Amata, I. / Gabel, F. / Simon, B. / Carlomagno, T.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of the K-turn U4 RNA: a combined NMR and SANS study.
Authors: Falb, M. / Amata, I. / Gabel, F. / Simon, B. / Carlomagno, T.
History
DepositionMay 12, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMay 26, 2010ID: 2KR8
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP* GP*GP*UP*U)-3'
B: 5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,6352
Polymers10,6352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST ENERGY STRUCTURES
RepresentativeModel #1

-
Components

#1: RNA chain 5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP* GP*GP*UP*U)-3' / U4 SNRNA 5' STEM LOOP / U4B SNRNA


Mass: 6118.682 Da / Num. of mol.: 1 / Fragment: U4 5'-SL STRAND A, RESIDUES 19-37 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: GenBank: 36174
#2: RNA chain 5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3' / U4 SNRNA 5' STEM LOOP / U4A SNRNA


Mass: 4516.764 Da / Num. of mol.: 1 / Fragment: U4 5'-SL STRAND B, RESIDUES 40-53 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: GenBank: 36174
Compound detailsENGINEERED RESIDUE IN CHAIN A, U 19 TO G ENGINEERED RESIDUE IN CHAIN B, U 40 TO G ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, U 19 TO G ENGINEERED RESIDUE IN CHAIN B, U 40 TO G ENGINEERED RESIDUE IN CHAIN B, U 53 TO C

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-15N HSQC
1313D HCN
2412D 1H-13C HSQC
2512D 1H-15N HSQC
2612D
3713D 13C-EDITED
38113C- FILTERED NOESY
3913D (H)CCH- COSY-TOCSY
31013D (H)CCH-E.COSY
41112D 15N HSQC
512115N- FILTERED NOESY
51313D HCN
61413D-HCP
61513D-ECOSY
61612D-HNN- COSY
71712D 15N-FILTERED NOESY
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 90% H2O/10% D2O, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120 7.6 1.0 atm298.0 K
2120 7.6 1.0 atm298.0 K
3120 7.6 1.0 atm298.0 K
4120 7.6 1.0 atm298.0 K
5120 7.6 1.0 atm278.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE6004
Bruker AVANCEBrukerAVANCE6005

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA-CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ARIA CNS 1.21.1structure solution
RefinementMethod: RDC REFINEMENT, WATER REFINEMENT / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES / Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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