5BJR

Crystal structure of the N-terminal RRM domain from MEC-8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family.

Soufari, H.Mackereth, C.D.

(2017) RNA 23: 308-316

  • DOI: https://doi.org/10.1261/rna.059733.116
  • Primary Citation of Related Structures:  
    5BJR, 5TKZ

  • PubMed Abstract: 

    Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets.


  • Organizational Affiliation

    University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mec-8 protein
A, B
94Caenorhabditis elegansMutation(s): 2 
Gene Names: mec-8CELE_F46A9.6F46A9.6
UniProt
Find proteins for G5ECJ4 (Caenorhabditis elegans)
Explore G5ECJ4 
Go to UniProtKB:  G5ECJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5ECJ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.59α = 90
b = 96.42β = 90
c = 109.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description