5MF9 | pdb_00005mf9

Solution structure of the RBM5 OCRE domain in complex with polyproline SmN peptide.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 5MF9

This is version 1.3 of the entry. See complete history

Literature

Structural basis for the recognition ofspliceosomal SmN B B proteins by theRBM5 OCRE domain in splicing regulation

Mourao, A.Bonnal, S.Komal, S.Warner, L.Bordonne, R.Valcarcel, J.Sattler, M.

(2016) Elife 5: 1-25

  • DOI: https://doi.org/10.7554/eLife.14707
  • Primary Citation Related Structures: 
    5MF9, 5MFY

  • PubMed Abstract: 

    The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95 , Caspase-2 and AID . An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique β-sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B'. The NMR structure of an OCRE-SmN peptide complex reveals a specific recognition of poly-proline helical motifs in SmN/B/B'. Mutation of conserved aromatic residues impairs binding to the Sm proteins in vitro and compromises RBM5-mediated alternative splicing regulation of FAS/CD95. Thus, RBM5 OCRE represents a poly-proline recognition domain that mediates critical interactions with the C-terminal tail of the spliceosomal SmN/B/B' proteins in FAS/CD95 alternative splicing regulation.


  • Organizational Affiliation
    • Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 8.57 kDa 
  • Atom Count: 607 
  • Modeled Residue Count: 75 
  • Deposited Residue Count: 75 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 564Homo sapiensMutation(s): 0 
Gene Names: RBM5H37LUCA15
UniProt & NIH Common Fund Data Resources
Find proteins for P52756 (Homo sapiens)
Explore P52756 
Go to UniProtKB:  P52756
PHAROS:  P52756
GTEx:  ENSG00000003756 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52756
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Survival motor neuron protein11Homo sapiensMutation(s): 0 
Gene Names: SMN1SMNSMNTSMN2SMNC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens)
Explore Q16637 
Go to UniProtKB:  Q16637
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16637
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1035
German Research FoundationGermanyGRK1721
Banco de SantanderSpainConsolider RNAREG, MICINN, AGAUR
Spanish Ministry of Economy and CompetitivenessSpainCentro de Excelencia Severo Ochoa 2013-2017, SEV-2012-0208

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-31
    Changes: Data collection
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references