PDBsum entry 3vak

RNA binding protein/DNA

PDB id: 3vak

Contents

Protein chains

174 a.a.

DNA/RNA

Ligands

DIO ×5

SO4 ×7

GOL ×4

CPQ

Waters ×272

PDB id:

3vak

Name:

RNA binding protein/DNA

Title:

Structure of u2af65 variant with bru5 DNA

Structure:

Splicing factor u2af 65 kda subunit. Chain: a, b. Fragment: RNA binding domains 1 and 2. Synonym: u2 auxiliary factor 65 kda subunit, hu2af(65), hu2af65, u2 snrnp auxiliary factor large subunit. Engineered: yes. DNA (5'-d( Up Up Up Up (Bru)p Up U)-3'). Chain: p, e. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: u2af2, u2af65. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.17Å R-factor: 0.192 R-free: 0.229

Authors:

J.L.Jenkins,C.L.Kielkopf

Key ref:

J.L.Jenkins et al. (2013). U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res, 41, 3859-3873. PubMed id: 23376934 DOI: 10.1093/nar/gkt046

Date:

29-Dec-11 Release date: 13-Feb-13

Protein chains

P26368  (U2AF2_HUMAN) -  Splicing factor U2AF 65 kDa subunit from Homo sapiens

Seq: 475 a.a.

Struc: 174 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

U-U-U-U-BRU-U-U 7 bases

U-U-U-U-BRU-U-U 7 bases

DOI no: 10.1093/nar/gkt046

Nucleic Acids Res 41:3859-3873 (2013)

PubMed id: 23376934

U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.

J.L.Jenkins, A.A.Agrawal, A.Gupta, M.R.Green, C.L.Kielkopf.

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).