2YH1

Model of human U2AF65 tandem RRM1 and RRM2 domains with eight-site uridine binding

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 125 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Multi-Domain Conformational Selection Underlies Pre-Mrna Splicing Regulation by U2Af

Mackereth, C.D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcarcel, J., Sattler, M.

(2011) Nature 475: 408

  • DOI: 10.1038/nature10171
  • Primary Citation of Related Structures:  
    2YH1, 2YH0

  • PubMed Abstract: 

    • Many cellular functions involve multi-domain proteins, which are composed of structurally independent modules connected by flexible linkers. Although it is often well understood how a given domain recognizes a cognate oligonucleotide or peptide motif ...

    Many cellular functions involve multi-domain proteins, which are composed of structurally independent modules connected by flexible linkers. Although it is often well understood how a given domain recognizes a cognate oligonucleotide or peptide motif, the dynamic interaction of multiple domains in the recognition of these ligands remains to be characterized. Here we have studied the molecular mechanisms of the recognition of the 3'-splice-site-associated polypyrimidine tract RNA by the large subunit of the human U2 snRNP auxiliary factor (U2AF65) as a key early step in pre-mRNA splicing. We show that the tandem RNA recognition motif domains of U2AF65 adopt two remarkably distinct domain arrangements in the absence or presence of a strong (that is, high affinity) polypyrimidine tract. Recognition of sequence variations in the polypyrimidine tract RNA involves a population shift between these closed and open conformations. The equilibrium between the two conformations functions as a molecular rheostat that quantitatively correlates the natural variations in polypyrimidine tract nucleotide composition, length and functional strength to the efficiency to recruit U2 snRNP to the intron during spliceosome assembly. Mutations that shift the conformational equilibrium without directly affecting RNA binding modulate splicing activity accordingly. Similar mechanisms of cooperative multi-domain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multi-domain proteins.

    Related Citations: 
    • Structural Basis for Polypyrimidine Tract Recognition by the Essential Pre-Mrna Splicing Factor U2Af65.
      Sickmier, E.A., Frato, K.E., Shen, H., Paranawithana, S.R., Green, M.R., Kielkopf, C.L.
      (2006) Mol Cell 23: 49
    Organizational Affiliation: 

    Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SPLICING FACTOR U2AF 65 KDA SUBUNITA198Homo sapiensMutation(s): 0 
Gene Names: U2AF2, U2AF65
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
NIH Common Fund Data Resources
PHAROS  P26368
GTEx  ENSG00000063244
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'B9Homo sapiens
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 125 
    • Conformers Submitted: 10 
    • Selection Criteria: LOWEST ENERGY 
    • OLDERADO: 2YH1 Olderado

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-07-20
      Type: Initial release
    • Version 1.1: 2011-07-27
      Changes: Atomic model, Database references, Other
    • Version 1.2: 2019-09-25
      Changes: Data collection, Other