PDBsum entry: 2dt6

RNA binding protein

PDB id: 2dt6

Contents

Protein chain

64 a.a. *

* Residue conservation analysis

PDB id:

2dt6

Name:

RNA binding protein

Title:

Solution structure of the first surp domain of human splicing factor sf3a120

Structure:

Splicing factor 3 subunit 1. Chain: a. Fragment: surp domain. Synonym: spliceosome-associated protein 114, sap 114, sf3a120. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: sf3a120, sf3a1. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

K.Kuwasako,F.He,M.Inoue,A.Tanaka,S.Sugano,P.Guentert,Y.Muto, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

K.Kuwasako et al. (2006). Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP. Structure, 14, 1677-1689. PubMed id: 17098193 DOI: 10.1016/j.str.2006.09.009

Date:

11-Jul-06 Release date: 26-Dec-06

Protein chain

Q15459  (SF3A1_HUMAN) -  Splicing factor 3A subunit 1

Seq: 793 a.a.

Struc: 64 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (1 term)
• Biochemical function: RNA binding (1 term)

DOI no: 10.1016/j.str.2006.09.009

Structure 14:1677-1689 (2006)

PubMed id: 17098193

Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP.

K.Kuwasako, F.He, M.Inoue, A.Tanaka, S.Sugano, P.Güntert, Y.Muto, S.Yokoyama.

ABSTRACT

The SF3a complex, consisting of SF3a60, SF3a66, and SF3a120, in 17S U2 snRNP is crucial to spliceosomal assembly. SF3a120 contains two tandem SURP domains (SURP1 and SURP2), and SURP2 is responsible for binding to SF3a60. We found that the SURP2 fragment forms a stable complex with an SF3a60 fragment (residues 71-107) and solved its structure by NMR spectroscopy. SURP2 exhibits a fold of the alpha1-alpha2-3(10)-alpha3 topology, and the SF3a60 fragment forms an amphipathic alpha helix intimately contacting alpha1 of SURP2. We also solved the SURP1 structure, which has the same fold as SURP2. The protein-binding interface of SURP2 is quite similar to the corresponding surface of SURP1, except for two amino acid residues. One of them, Leu169, is characteristic of SF3a120 SURP2 among SURP domains. Mutagenesis showed that this single Leu residue is the critical determinant for complex formation, which reveals the protein recognition mechanism in the subunit assembly.

Selected figure(s)

Figure 1.
Figure 1. Sequence Alignment of SURP1 and SURP2 in SF3a120 and SURP1 in Human SWAP
Yellow backgrounds and asterisks indicate highly conserved residues among the SURP domains, and a black background with yellow letters indicates the conserved phenylalanine among all of the SURP domains, as shown in Figure 8B. The critical position for complex formation is indicated by a red arrowhead, and the colors reflect the amino acid type: red, blue, and green letters represent hydrophobic (protein-binding type), charged, and neutral (S, T, and Q) amino acids, respectively. The hydrophobic-core-forming residues are indicated by filled circles, and the residues that interact with the core residues are indicated by open circles. Red stars and red open stars indicate the hydrophobic- and hydrophilic-complex-forming residues in SURP2 of SF3a120, respectively.

Figure 8.
Figure 8. Sequence Profiling Analyses of SURP Domains
(A) SURP-containing proteins in eukaryotes.
(B) HMM-logo format representation of the amino acid conservation in the SURP domains. The sequence information of all of the SURP domains shown in (A) was analyzed by the HMMER program (Schuster-Bockler et al., 2004). Asterisks indicate highly conserved residues among the SURP domains. The red arrowhead indicates the critical position for the complex formation.
(C) Phylogenic tree of the SURP domains. All of the SURP domains shown in (A) are included. The colors of the letters reflect the amino acid type of the critical residues for the complex formation (Leu169 in the SURP2 domain on human SF3a120); red, blue, and green letters represent hydrophobic (protein-binding type), charged, and neutral (S, T, and Q) amino acids in the positions, respectively.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1677-1689) copyright 2006.

Figures were selected by an automated process.