2M09 | pdb_00002m09

Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition

• PDB DOI: https://doi.org/10.2210/pdb2M09/pdb
• BMRB: 18802

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-22 Released: 2013-01-30 
• Deposition Author(s): Madl, T., Sattler, M., Zhang, Y., Bagdiul, I., Kern, T., Kang, H., Zou, P., Maeusbacher, N., Sieber, S.A., Kraemer, A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition.

Zhang, Y., Madl, T., Bagdiul, I., Kern, T., Kang, H.S., Zou, P., Mausbacher, N., Sieber, S.A., Kramer, A., Sattler, M.

(2013) Nucleic Acids Res 41: 1343-1354

• PubMed: 23175611 
• DOI: https://doi.org/10.1093/nar/gks1097
• Primary Citation Related Structures: 
  2M09, 2M0G


• PubMed Abstract: 
  

  Recognition of the 3'-splice site is a key step in pre-mRNA splicing and accomplished by a dynamic complex comprising splicing factor 1 (SF1) and the U2 snRNP auxiliary factor 65-kDa subunit (U2AF65). Both proteins mediate protein-protein and protein-RNA interactions for cooperative RNA-binding during spliceosome assembly. Here, we report the solution structure of a novel helix-hairpin domain in the N-terminal region of SF1 (SF1(NTD)). The nuclear magnetic resonance- and small-angle X-ray scattering-derived structure of a complex of the SF1(NTD) with the C-terminal U2AF homology motif domain of U2AF65 (U2AF65(UHM)) reveals that, in addition to the known U2AF65(UHM)-SF1 interaction, the helix-hairpin domain forms a secondary, hydrophobic interface with U2AF65(UHM), which locks the orientation of the two subunits. Mutational analysis shows that the helix hairpin is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. We further show that tandem serine phosphorylation of a conserved Ser80-Pro81-Ser82-Pro83 motif rigidifies a long unstructured linker in the SF1 helix hairpin. Phosphorylation does not significantly alter the overall conformations of SF1, SF1-U2AF65 or the SF1-U2AF65-RNA complexes, but slightly enhances RNA binding. Our results indicate that the helix-hairpin domain of SF1 is required for cooperative 3'-splice site recognition presumably by stabilizing a unique quaternary arrangement of the SF1-U2AF65-RNA complex.

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Organizational Affiliation: 
• Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.82 kDa 
• Atom Count: 969 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 1	A	121	Homo sapiens	Mutation(s): 0  Gene Names: SF1, ZFM1, ZNF162
UniProt & NIH Common Fund Data Resources
Find proteins for Q15637 (Homo sapiens) Explore Q15637  Go to UniProtKB:  Q15637
PHAROS:  Q15637 GTEx:  ENSG00000168066

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Madl, T., Sattler, M., Zhang, Y., Bagdiul, I., Kern, T., Kang, H., Zou, P., Maeusbacher, N., Sieber, S.A., Kraemer, A.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references