PDBsum entry 2peh

Protein binding

PDB id: 2peh

Contents

Protein chains

104 a.a. *

Ligands

LYS-ARG-LYS-SER-ARG-TRP-ASP-GLU-THR-PRO

ARG-LYS-SER-ARG-TRP-ASP-GLU-THR-PRO

Waters ×93

* Residue conservation analysis

PDB id:

2peh

Name:

Protein binding

Title:

Crystal structure of the uhm domain of human spf45 in complex with sf3b155-ulm5

Structure:

Splicing factor 45. Chain: a, b. Synonym: 45 kda-splicing factor, RNA-binding motif protein 17. Engineered: yes. Splicing factor 3b subunit 1. Chain: c, d. Synonym: spliceosome-associated protein 155, sap 155, sf3b155, pre- mRNA-splicing factor sf3b 155 kda subunit. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rbm17, spf45. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the sf3b 155 peptide was chemically synthesized

Resolution:

2.11Å R-factor: 0.211 R-free: 0.273

Authors:

L.Corsini,J.Basquin,M.Hothorn,M.Sattler

Key ref:

L.Corsini et al. (2007). U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Nat Struct Biol, 14, 620-629. PubMed id: 17589525 DOI: 10.1038/nsmb1260

Date:

03-Apr-07 Release date: 26-Jun-07

Protein chains

Q96I25  (SPF45_HUMAN) -  Splicing factor 45 from Homo sapiens

Seq: 401 a.a.

Struc: 104 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1038/nsmb1260

Nat Struct Biol 14:620-629 (2007)

PubMed id: 17589525

U2AF-homology motif interactions are required for alternative splicing regulation by SPF45.

L.Corsini, S.Bonnal, S.Bonna, J.Basquin, M.Hothorn, K.Scheffzek, J.Valcárcel, M.Sattler.

ABSTRACT

The U2AF-homology motif (UHM) mediates protein-protein interactions between factors involved in constitutive RNA splicing. Here we report that the splicing factor SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also called CD95). The SPF45 UHM is necessary for this activity and binds UHM-ligand motifs (ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. We describe a 2.1-A crystal structure of SPF45-UHM in complex with a ULM peptide from SF3b155. Features distinct from those of previously described UHM-ULM structures allowed the design of mutations in the SPF45 UHM that selectively impair binding to individual ULMs. Splicing assays using the ULM-selective SPF45 variants demonstrate that individual UHM-ULM interactions are required for FAS splicing regulation by SPF45 in vivo. Our data suggest that networks of UHM-ULM interactions are involved in regulating alternative splicing.

Selected figure(s)

Figure 1.
(a) Domain alignment of proteins that contain a UHM. (b) Alignment of ULM sequences in U2AF65, SF1 and SF3b155. Conserved residues are colored as follows: blue, basic residues preceding conserved tryptophan; yellow, conserved tryptophan; orange, acidic and Asn/Gln-type residues following tryptophan; green, conserved and potentially phosphorylated serine and threonine residues; purple, proline adjacent to threonine. (c) Schematic drawing of 3' splice sites in spliceosomal complexes E and A.

Figure 4.
(a) Ribbon representation of SPF45-UHM with stick representation of SF3b155-ULM5 peptide. (b) Details of the molecular recognition of SPF45-UHM and SF3b155-ULM5. Experimental omit-electron density map contoured at 1.8 (blue) surrounds a stick representation of residues 337–342 of the SF3b155 peptide (orange). SPF45-UHM residues involved in ULM coordination are shown in gray. (c) Structures of the U2AF65-UHM–SF1-ULM complex (left, PDB 1O0P) and the U2AF35-UHM–U2AF65-ULM complex (right, PDB 1JMT).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2007, 14, 620-629) copyright 2007.

Figures were selected by an automated process.