[English] 日本語
Yorodumi
- PDB-7zap: Solution structure of RBM39 RRM1 bound to U1 snRNA stem loop 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zap
TitleSolution structure of RBM39 RRM1 bound to U1 snRNA stem loop 3
Components
  • RNA-binding protein 39
  • U1 snRNA SL3
KeywordsRNA BINDING PROTEIN / RBM39 / RRM / stem loop recognition
Function / homology
Function and homology information


mRNA processing / RNA binding / nucleus
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / 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 (> 10) / RNA binding motif protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCampagne, S. / Allain, F.H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.
Authors: Campagne, S. / Jutzi, D. / Malard, F. / Matoga, M. / Romane, K. / Feldmuller, M. / Colombo, M. / Ruepp, M.D. / Allain, F.H.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein 39
B: U1 snRNA SL3


Theoretical massNumber of molelcules
Total (without water)19,7752
Polymers19,7752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, Co-purification, gel shifts
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein RNA-binding protein 39 / RNA-binding region (RNP1 / RRM) containing 2 / isoform CRA_f


Mass: 10820.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM39, RNPC2, hCG_38221 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XAC6
#2: RNA chain U1 snRNA SL3


Mass: 8954.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic32D 1H-13C HSQC
131isotropic33D HN(CA)CB
141isotropic33D CBCA(CO)NH
151isotropic33D HNCO
161isotropic33D HNCA
171isotropic23D H(CCO)NH
181isotropic23D C(CO)NH
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic
1122isotropic23D (H)CCH-TOCSY
1132isotropic23D edited filtered 1H-13C NOESY HSQC
1142isotropic22D 1H-1H F1f NOESY
1152isotropic22D 1H-1H F2fF1F NOESY
1163isotropic22D 1H-13C HSQC
1173isotropic12D 1H-1H NOESY
1183isotropic13D 1H-13C NOESY aliphatic
1193isotropic13D 1H-13C NOESY aromatic
1203isotropic23D 1H-13C edited-filtered NOESY HSQC
1213isotropic23D (H)CCH-COSY
1223isotropic23D (H)CCH-TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution110 mM sodium phosphate, 3 mM DTT, 1.2 mM [U-13C; U-15N] RBM39 RRM1, 1.5 mM U1 snRNA SL3, 90% H2O/10% D2O13C15N-labelled RBM39 RRM1 +1,2 equivalent of unlabelled U1 snRNA SL3 1,2 mM NaPO4 10mM pH5,5 DTT 3 mM13C15N-protein-Un-SL390% H2O/10% D2O
solution210 mM sodium phosphate, 3 mM DTT, 1.2 mM [U-13C; U-15N] RBM39 RRM1, 1.5 mM U1 snRNA SL3, 100% D2O13C15N-labelled RBM39 RRM1 +1,2 equivalent of unlabelled U1 snRNA SL3 1,2 mM NaPO4 10mM pH5,5 DTT 3 mM13C15N-protein-Un-SL3_in_D20100% D2O
solution310 mM sodium phosphate, 3 mM DTT, 1.2 mM [U-13C; U-15N] RBM39 RRM1, 1.5 mM U1 snRNA SL3, 100% D2O13C15N-labelled RBM39 RRM1 +1,2 equivalent of unlabelled U1 snRNA SL3 1,2 mM NaPO4 10mM pH5,5 DTT 3 mM13C15N-SL3-Un-RBM39 RRM1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
3 mMDTTnatural abundance1
1.2 mMRBM39 RRM1[U-13C; U-15N]1
1.5 mMU1 snRNA SL3natural abundance1
10 mMsodium phosphatenatural abundance2
3 mMDTTnatural abundance2
1.2 mMRBM39 RRM1[U-13C; U-15N]2
1.5 mMU1 snRNA SL3natural abundance2
10 mMsodium phosphatenatural abundance3
3 mMDTTnatural abundance3
1.2 mMRBM39 RRM1[U-13C; U-15N]3
1.5 mMU1 snRNA SL3natural abundance3
Sample conditionsDetails: NaPO4 10mM pH5,5 DTT 3 mM 313 K / Ionic strength: 10 mM / Label: conditions_1 / pH: 5.5 / PH err: 0.1 / Pressure: atmospheric atm / Temperature: 313 K / Temperature err: 0

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE NEOBrukerAVANCE NEO7002
Bruker AVANCE NEOBrukerAVANCE NEO6003

-
Processing

NMR software
NameVersionDeveloperClassification
Amber21Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
ATNOSThorsten Hermannpeak picking
TopSpinBruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / 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://pdbjlc1.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