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: 2.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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
  • Structures With Same Primary Citation

  • 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 Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 39A, C, E, G, I, K, M, O, Q114Mus musculusMutation(s): 1 
Gene Names: Rbm39CaperRnpc2
Find proteins for Q8VH51 (Mus musculus)
Explore Q8VH51 
Go to UniProtKB:  Q8VH51
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 65 kDa subunitB, D, F, H, J, L, N, P, R29Mus musculusMutation(s): 0 
Gene Names: U2af2U2af65
Find proteins for P26369 (Mus musculus)
Explore P26369 
Go to UniProtKB:  P26369
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 32
  • Diffraction Data DOI: 10.18430/M35CXT Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.283α = 90
b = 127.283β = 90
c = 78.864γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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