[English] 日本語
Yorodumi
- PDB-6so9: Mouse RBM20 RRM domain in complex with AUCUUA RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6so9
TitleMouse RBM20 RRM domain in complex with AUCUUA RNA
Components
  • AUCUUA
  • RNA-binding protein 20
KeywordsRNA BINDING PROTEIN / Alternative splicing
Function / homology
Function and homology information


spliceosome-depend formation of circular RNA / heart formation / splicing factor binding / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / pre-mRNA intronic binding / positive regulation of RNA splicing / cytoplasmic ribonucleoprotein granule / RNA binding / zinc ion binding / nucleus
Similarity search - Function
RBM20, RNA recognition motif / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA-binding protein 20
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMackereth, C.D. / Upadhyay, S.K.
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of UCUU RNA motif recognition by splicing factor RBM20.
Authors: Upadhyay, S.K. / Mackereth, C.D.
#1: Journal: Biorxiv / Year: 2019
Title: Structural basis of UCUU RNA motif recognition by splicing factor RBM20
Authors: Mackereth, C.D. / Upadhyay, S.K.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_validate_polymer_linkage
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: AUCUUA
A: RNA-binding protein 20


Theoretical massNumber of molelcules
Total (without water)14,3292
Polymers14,3292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2010 Å2
ΔGint-7 kcal/mol
Surface area7220 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain AUCUUA


Mass: 1757.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein RNA-binding protein 20 / RNA-binding motif protein 20


Mass: 12571.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbm20 / Plasmid: pET-His1a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): lysY / References: UniProt: Q3UQS8
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
125isotropic22D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HNCA
161isotropic13D CBCA(CO)NH
171isotropic13D HNHA
181isotropic13D (H)CCH-TOCSY
191isotropic13D (H)CCH-TOCSY
1106isotropic12D 1H-13C HSQC CT
1112isotropic13D 1H-15N NOESY
1125isotropic23D 1H-13C NOESY
1135isotropic22D 1H-13C HSQC aromatic
1144isotropic22D 1H-1H NOESY
1154isotropic22D 1H-1H TOCSY
2167isotropic12D x2-filtered 1H-1H NOESY
1174isotropic12D 1H-13C HSQC
1185isotropic22D x2-filtered 1H-1H NOESY
1191isotropic13D (H)C(CO)NH-TOCSY
1206isotropic12D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1400 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O13C,15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA13C15N_H2O90% H2O/10% D2O
solution2400 uM [U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA15N_H2O90% H2O/10% D2O
solution3500 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 600 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O13C15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA13C15N_H2O_290% H2O/10% D2O
solution4300 uM [U-99% 2H; U-99% 15N] Mouse RBM20 RRM domain, 290 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O2H15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA2H15N_D2O100% D2O
solution5300 uM [U-99% 13C] Mouse RBM20 RRM domain, 360 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O13C-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA13C_D2O100% D2O
solution6450 uM [U-10% 13C; U-99% 15N] Mouse RBM20 RRM domain, 560 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O10%-13C,15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA10%C_H2O90% H2O/10% D2O
solution7500 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 600 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O13C15N-labelled RBM20(513-621) in complex with natural abundance AUCUUA RNA13C15N_H2O_27890% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMMouse RBM20 RRM domain[U-99% 13C; U-99% 15N]1
480 uMAUCUUAnatural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
400 uMMouse RBM20 RRM domain[U-99% 15N]2
480 uMAUCUUAnatural abundance2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
500 uMMouse RBM20 RRM domain[U-99% 13C; U-99% 15N]3
600 uMAUCUUAnatural abundance3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
300 uMMouse RBM20 RRM domain[U-99% 2H; U-99% 15N]4
290 uMAUCUUAnatural abundance4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
300 uMMouse RBM20 RRM domain[U-99% 13C]5
360 uMAUCUUAnatural abundance5
20 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
450 uMMouse RBM20 RRM domain[U-10% 13C; U-99% 15N]6
560 uMAUCUUAnatural abundance6
20 mMsodium phosphatenatural abundance6
50 mMsodium chloridenatural abundance6
500 uMMouse RBM20 RRM domain[U-99% 13C; U-99% 15N]7
600 uMAUCUUAnatural abundance7
20 mMsodium phosphatenatural abundance7
50 mMsodium chloridenatural abundance7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
170 mM298K6.51 atm298 K
270 mM278K6.51 atm278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker NeoBrukerNeo7001TXI
Bruker AVANCE IIIBrukerAVANCE III8002cryoprobe TCI

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinalDetails
simulated annealing4ARIA 2.3
simulated annealing5CNS 1.2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

+
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