ISDA

Deposition Date 2020-04-30

Release Date 2020-09-30

Last Version Date 2023-11-29

Entry Detail

PDB ID:

7C06

Keywords:

SPLICING/RNA

Title:

Crystal structure of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.

Biological Source:

Source Organism:

Schizosaccharomyces pombe 972h- (Taxon ID: 284812)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.02 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor U2AF 23 kDa subunit
Gene (Uniprot):SPAP8A3.06
Chain IDs:A, D, G, J, M, P, S, V, Y
Chain Length:216
Number of Molecules:9
Biological Source:Schizosaccharomyces pombe 972h-

UniProt ID:Q09176 Pfam ID:PF00642, PF00076

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor U2AF 59 kDa subunit
Gene (Uniprot):prp2
Chain IDs:B, E, H, K, N, Q, T, W, Z
Chain Length:69
Number of Molecules:9
Biological Source:Schizosaccharomyces pombe 972h-

UniProt ID:P36629

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
Chain IDs:C, F, I, L, O, R, U, X, AA (auth: 1)
Chain Length:6
Number of Molecules:9
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.

Yoshida, H, Park, S.Y, Sakashita, G, Nariai, Y, Kuwasako, K, Muto, Y, Urano, T, Obayashi, E.Show

Nat Commun 11 4744 4744 (2020)

PMID: 32958768 DOI: 10.1038/s41467-020-18559-6

Abstact

The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors.

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Protein

Chemical

Disease

Primary Citation of related structures