[English] 日本語
Yorodumi
- PDB-6snj: Solution structure of the FUS/TLS RNA recognition motif in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6snj
TitleSolution structure of the FUS/TLS RNA recognition motif in complex with U1 snRNA stem loop III
Components
  • RNA-binding protein FUS
  • U1 snRNA stem loop III, RNA (28-MER)
KeywordsSPLICING / Splicing regulation / FUS-U1snRNP / Spliceosome
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / 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 protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCampagne, S. / Allain, F.H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_170130 Switzerland
CitationJournal: Nat Commun / Year: 2020
Title: Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis.
Authors: Jutzi, D. / Campagne, S. / Schmidt, R. / Reber, S. / Mechtersheimer, J. / Gypas, F. / Schweingruber, C. / Colombo, M. / von Schroetter, C. / Loughlin, F.E. / Devoy, A. / Hedlund, E. / ...Authors: Jutzi, D. / Campagne, S. / Schmidt, R. / Reber, S. / Mechtersheimer, J. / Gypas, F. / Schweingruber, C. / Colombo, M. / von Schroetter, C. / Loughlin, F.E. / Devoy, A. / Hedlund, E. / Zavolan, M. / Allain, F.H. / Ruepp, M.D.
History
DepositionAug 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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-binding protein FUS
B: U1 snRNA stem loop III, RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)23,0922
Polymers23,0922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2810 Å2
ΔGint-11 kcal/mol
Surface area11510 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein RNA-binding protein FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 14137.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon+ / References: UniProt: P35637
#2: RNA chain U1 snRNA stem loop III, RNA (28-MER)


Mass: 8954.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-13C HSQC aliphatic
152isotropic12D 1H-13C HSQC aromatic
1141isotropic33D 1H-15N NOESY
1131isotropic33D 1H-13C NOESY aliphatic
1121isotropic33D 1H-13C NOESY aromatic
1112isotropic23D 1H-13C NOESY aliphatic
1102isotropic23D 1H-13C NOESY aromatic
193isotropic32D 1H-13C HSQC aliphatic
183isotropic32D 1H-13C HSQC aromatic
173isotropic33D 1H-13C NOESY
163isotropic23D (H)CCH-TOCSY
1191isotropic13D HN(CA)CB
1181isotropic13D CBCA(CO)NH
1171isotropic13D HNCO
1161isotropic13D HNCA
1154isotropic32D 1H-1H NOESY
1222isotropic22D F1FF2f NOESY
1212isotropic22D F2F NOEY
1202isotropic22D F1fF2F TOCSY
1242isotropic33D 1H-13C filtered edited NOESY HSQC
1233isotropic33D 1H-13C filtered edited NOESY HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.2 mM [U-99% 13C; U-99% 15N] FUS/TLS RNA recognition motif (260-390), 1.5 mM SL3, 10 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2OFUS/TLS RRM 13C15N labeled in complex with U1snRNA SL315N_13C_sample_H2090% H2O/10% D2O
solution21.2 mM [U-99% 13C; U-99% 15N] FUS/TLS RNA recognition motif (260-390), 1.5 mM SL3, 10 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100% D2OFUS/TLS RRM 13C15N labeled in complex with U1snRNA SL3 in D2015N_13C_sample_D20100% D2O
solution31 mM FUS/TLS RNA recognition motif (260-390), 0.8 mM [U-13C; U-15N] SL3, 10 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100% D2OFUS/TLS RRM unlabeled in complex with U1snRNA SL3 13C15N in D20RNA_labeled100% D2O
solution41 mM FUS/TLS RNA recognition motif (260-390), 1 mM SL3, 10 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2OFUS/TLS RRM in complex with U1snRNA SL3 in H20UN90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMFUS/TLS RNA recognition motif (260-390)[U-99% 13C; U-99% 15N]1
1.5 mMSL3natural abundance1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
1.2 mMFUS/TLS RNA recognition motif (260-390)[U-99% 13C; U-99% 15N]2
1.5 mMSL3natural abundance2
10 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
1 mMFUS/TLS RNA recognition motif (260-390)natural abundance3
0.8 mMSL3[U-13C; U-15N]3
10 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
1 mMFUS/TLS RNA recognition motif (260-390)natural abundance4
1 mMSL3natural abundance4
10 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
Sample conditionsIonic strength: 60 mM / Label: 1 / pH: 6.8 / PH err: 0.1 / Pressure: atm atm / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001cryo-probbed
Bruker AVANCE IIIBrukerAVANCE III7002cryo-probbed
Bruker AVANCEBrukerAVANCE9003cryo-probbed

-
Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 18

+
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