5CXT

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.

Stepanyuk, G.A.Serrano, P.Peralta, E.Farr, C.L.Axelrod, H.L.Geralt, M.Das, D.Chiu, H.J.Jaroszewski, L.Deacon, A.M.Lesley, S.A.Elsliger, M.A.Godzik, A.Wilson, I.A.Wuthrich, K.Salomon, D.R.Williamson, J.R.

(2016) Acta Crystallogr D Struct Biol 72: 497-511

  • DOI: 10.1107/S2059798316001248

  • PubMed Abstract: 
  • RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belo ...

    RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.


    Organizational Affiliation

    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Joint Center for Structural Genomics, http://www.jcsg.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 39
A, C, E, G, I, K, M, O, Q
114Mus musculusMutation(s): 1 
Gene Names: Rbm39 (Caper, Rnpc2)
Find proteins for Q8VH51 (Mus musculus)
Go to UniProtKB:  Q8VH51
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 65 kDa subunit
B, D, F, H, J, L, N, P, R
29Mus musculusMutation(s): 0 
Gene Names: U2af2 (U2af65)
Find proteins for P26369 (Mus musculus)
Go to UniProtKB:  P26369
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 127.283α = 90.00
b = 127.283β = 90.00
c = 78.864γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Derived calculations
  • Version 1.2: 2016-04-20
    Type: Database references