3VAJ

Structure of U2AF65 variant with BrU5C6 DNA

Summary for 3VAJ

• Entry DOI: 10.2210/pdb3vaj/pdb
• Related: 2G4B 2HZC 3VAF 3VAG 3VAH 3VAI 3VAK 3VAL 3VAM 3VAN 3VAO
• Descriptor: Splicing factor U2AF 65 kDa subunit, DNA (5'-D(*UP*UP*UP*UP*(BRU)P*CP*U)-3'), 1,4-DIETHYLENE DIOXIDE, ... (7 entities in total)
• Functional Keywords: rna splicing factor, rna recognition motif, rna binding protein, rna binding protein-dna complex, rna binding protein/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P26368
• Total number of polymer chains: 4
• Total formula weight: 44342.90

Authors

Jenkins, J.L.,Kielkopf, C.L. (deposition date: 2011-12-29, release date: 2013-02-13, Last modification date: 2024-02-28)

Primary citation

Jenkins, J.L.,Agrawal, A.A.,Gupta, A.,Green, M.R.,Kielkopf, C.L.
U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Nucleic Acids Res., 41:3859-3873, 2013

PubMed Abstract: Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts preceding 3' splice sites while adapting to both cytidine and uridine nucleotides with nearly equivalent frequencies. To understand how U2AF(65) recognizes degenerate Py tracts, we determined six crystal structures of human U2AF(65) bound to cytidine-containing Py tracts. As deoxy-ribose backbones were required for co-crystallization with these Py tracts, we also determined two baseline structures of U2AF(65) bound to the deoxy-uridine counterparts and compared the original, RNA-bound structure. Local structural changes suggest that the N-terminal RNA recognition motif 1 (RRM1) is more promiscuous for cytosine-containing Py tracts than the C-terminal RRM2. These structural differences between the RRMs were reinforced by the specificities of wild-type and site-directed mutant U2AF(65) for region-dependent cytosine- and uracil-containing RNA sites. Small-angle X-ray scattering analyses further demonstrated that Py tract variations select distinct inter-RRM spacings from a pre-existing ensemble of U2AF(65) conformations. Our results highlight both local and global conformational selection as a means for universal 3' splice site recognition by U2AF(65).

PubMed: 23376934
DOI: 10.1093/nar/gkt046

Experimental method

X-RAY DIFFRACTION (1.9 Å)