[English] 日本語
Yorodumi
- PDB-6va3: Solution Structure of the Tau pre-mRNA Exon 10 Splicing Regulator... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6va3
TitleSolution Structure of the Tau pre-mRNA Exon 10 Splicing Regulatory Element Bound to MQC
Components
  • RNA (5'-R(*CP*AP*CP*AP*CP*GP*UP*CP*GP*G)-3')
  • RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*UP*GP*UP*G)-3')
KeywordsRNA / Adenine bulge / RNA complex / A-form tau RNA hairpin
Function / homologyChem-MQC / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, J.L. / Fountain, M.A. / Disney, M.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM097455-07 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)DP1-NS096898 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)P01-NS099114 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing.
Authors: Chen, J.L. / Zhang, P. / Abe, M. / Aikawa, H. / Zhang, L. / Frank, A.J. / Zembryski, T. / Hubbs, C. / Park, H. / Withka, J. / Steppan, C. / Rogers, L. / Cabral, S. / Pettersson, M. / Wager, ...Authors: Chen, J.L. / Zhang, P. / Abe, M. / Aikawa, H. / Zhang, L. / Frank, A.J. / Zembryski, T. / Hubbs, C. / Park, H. / Withka, J. / Steppan, C. / Rogers, L. / Cabral, S. / Pettersson, M. / Wager, T.T. / Fountain, M.A. / Rumbaugh, G. / Childs-Disney, J.L. / Disney, M.D.
History
DepositionDec 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*UP*GP*UP*G)-3')
B: RNA (5'-R(*CP*AP*CP*AP*CP*GP*UP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0203
Polymers6,7142
Non-polymers3061
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1350 Å2
ΔGint-5 kcal/mol
Surface area4200 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

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


Mass: 3538.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (5'-R(*CP*AP*CP*AP*CP*GP*UP*CP*GP*G)-3')


Mass: 3175.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MQC / 4-[(3-methoxyphenyl)amino]-2-methylquinoline-6-carboximidamide


Mass: 306.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1D2O 2D 1H-1H NOESY
131isotropic1D2O 2D DQF-COSY
222isotropic2H2O 2D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM WT Tau RNA, 0.6 mM MQC, 10 mM KH2PO4/K2HPO4, 0.05 mM EDTA, 100% D2OD2O_sample100% D2O
solution20.4 mM WT Tau RNA, 0.6 mM MQC, 10 mM KH2PO4/K2HPO4, 0.05 mM EDTA, 95% H2O/5% D2OH2O_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMWT Tau RNAnatural abundance1
0.6 mMMQCnatural abundance1
10 mMKH2PO4/K2HPO4natural abundance1
0.05 mMEDTAnatural abundance1
0.4 mMWT Tau RNAnatural abundance2
0.6 mMMQCnatural abundance2
10 mMKH2PO4/K2HPO4natural abundance2
0.05 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMconditions_D2O6.0 1 atm308 K
210 mMconditions_H2O6.0 1 atm278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8502

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / 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