1K1G | pdb_00001k1g

STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY SPLICING FACTOR 1

• PDB DOI: https://doi.org/10.2210/pdb1K1G/pdb
• NAKB: 1K1G

• Classification: GENE REGULATION/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-09-25 Released: 2001-11-07 
• Deposition Author(s): Liu, Z., Luyten, I., Bottomley, M.J., Messias, A.C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Kramer, A., Sattler, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: 10 lowest energy structures consistent with experimental distance and dihedral angle restraints 

Literature

Structural basis for recognition of the intron branch site RNA by splicing factor 1.

Liu, Z., Luyten, I., Bottomley, M.J., Messias, A.C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Kramer, A., Sattler, M.

(2001) Science 294: 1098-1102

• PubMed: 11691992 
• DOI: https://doi.org/10.1126/science.1064719
• Primary Citation Related Structures: 
  1K1G


• PubMed Abstract: 
  

  During spliceosome assembly, splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hn RNP K) fold which is necessary and sufficient for BPS binding. The 3' part of the BPS (UAAC), including the conserved branch point adenosine (underlined), is specifically recognized in a hydrophobic cleft formed by the Gly-Pro-Arg-Gly motif and the variable loop of the KH domain. The QUA2 region recognizes the 5' nucleotides of the BPS (ACU). The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A.

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Organizational Affiliation: 
• European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.16 kDa 
• Atom Count: 1,186 
• Modeled Residue Count: 133 
• Deposited Residue Count: 142 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SF1-Bo isoform	B [auth A]	131	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15637 (Homo sapiens) Explore Q15637  Go to UniProtKB:  Q15637
PHAROS:  Q15637 GTEx:  ENSG00000168066

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*A)-3'	A [auth B]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: 10 lowest energy structures consistent with experimental distance and dihedral angle restraints 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-07 
Deposition Author(s): Liu, Z., Luyten, I., Bottomley, M.J., Messias, A.C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Kramer, A., Sattler, M.

Revision History  

• Version 1.0: 2001-11-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection