[English] 日本語
Yorodumi
- PDB-7vrl: Solution structure of Rbfox RRM bound to a non-cognate RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vrl
TitleSolution structure of Rbfox RRM bound to a non-cognate RNA
Components
  • RNA (5'-R(*UP*GP*CP*AP*UP*AP*U)-3')
  • RNA binding protein fox-1 homolog 1
KeywordsRNA BINDING PROTEIN/RNA / RRM / non-cognate binding / splicing factor / complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / trans-Golgi network / mRNA processing / cytoplasmic stress granule / nervous system development / mRNA binding ...RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / trans-Golgi network / mRNA processing / cytoplasmic stress granule / nervous system development / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA binding protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, RNA recognition motif / 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
Similarity search - Domain/homology
RNA / RNA binding protein fox-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, F. / Varani, G.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2023
Title: Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity.
Authors: Ye, X. / Yang, W. / Yi, S. / Zhao, Y. / Varani, G. / Jankowsky, E. / Yang, F.
History
DepositionOct 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 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(*UP*GP*CP*AP*UP*AP*U)-3')
B: RNA binding protein fox-1 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,8702
Polymers13,8702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1790 Å2
ΔGint2 kcal/mol
Surface area8420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 2182.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein RNA binding protein fox-1 homolog 1 / Ataxin-2-binding protein 1 / Fox-1 homolog A / Hexaribonucleotide-binding protein 1


Mass: 11687.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFOX1, A2BP, A2BP1, FOX1, HRNBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWB1
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D 1H-15N NOESY
132isotropic23D 1H-13C NOESY
142isotropic13D NHCACB
152isotropic13D CBCA(CO)NH
162isotropic13D HNCO
172isotropic13D NH(CA)CO
1102isotropic13D HBHA(CO)NH
193isotropic13D (H)CCH-TOCSY
183isotropic12D 1H-13C HSQC
1113isotropic22D F1-F2- filtered NOESY
1123isotropic22D TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] protein, 1.2 mM unlabeled RNA, 10 mM unlabeled sodium phosphate, 30 mM unlabeled sodium chloride, 0.05 % w/v unlabeled sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] protein, 1.2 mM unlabeled RNA, 10 mM unlabeled sodium phosphate, 30 mM unlabeled sodium chloride, 0.05 % w/v unlabeled sodium azide, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution31 mM [U-15N, U-13C] protein, 1.2 mM unlabeled RNA, 10 mM unlabeled sodium phosphate, 30 mM unlabeled sodium chloride, 0.05 % w/v unlabeled sodium azide, 100% D2O15N13C_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-15N]1
1.2 mMRNAunlabeled1
10 mMsodium phosphateunlabeled1
30 mMsodium chlorideunlabeled1
0.05 % w/vsodium azideunlabeled1
1 mMprotein[U-13C; U-15N]2
1.2 mMRNAunlabeled2
10 mMsodium phosphateunlabeled2
30 mMsodium chlorideunlabeled2
0.05 % w/vsodium azideunlabeled2
1 mMprotein[U-15N, U-13C]3
1.2 mMRNAunlabeled3
10 mMsodium phosphateunlabeled3
30 mMsodium chlorideunlabeled3
0.05 % w/vsodium azideunlabeled3
Sample conditionsIonic strength: 40 mM / Label: condition_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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