2KXN

NMR structure of human Tra2beta1 RRM in complex with AAGAAC RNA

• PDB DOI:  https://doi.org/10.2210/pdb2KXN/pdb
• BMRB: 16920
• NAKB: 2KXN

• Classification: RNA binding protein/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-05-10 Released: 2011-03-16 
• Deposition Author(s): Clery, A., Jayne, S., Benderska, N., Dominguez, C., Stamm, S., Allain, F.H.-T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 

Literature

Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-beta1

Clery, A., Jayne, S., Benderska, N., Dominguez, C., Stamm, S., Allain, F.H.

(2011) Nat Struct Mol Biol 18: 443-450

• PubMed: 21399644 
• DOI: https://doi.org/10.1038/nsmb.2001
• Primary Citation of Related Structures:  
  2KXN


• PubMed Abstract: 
  

Tra2-β1 is a unique splicing factor as its single RNA recognition motif (RRM) is located between two RS (arginine-serine) domains. To understand how this protein recognizes its RNA target, we solved the structure of Tra2-β1 RRM in complex with RNA. The central 5'-AGAA-3' motif is specifically recognized by residues from the β-sheet of the RRM and by residues from both extremities flanking the RRM. The structure suggests that RNA binding by Tra2-β1 induces positioning of the two RS domains relative to one another. By testing the effect of Tra2-β1 and RNA mutations on the splicing of SMN2 exon 7, we validated the importance of the RNA-protein contacts observed in the structure for the function of Tra2-β1 and determined the functional sequence of Tra2-β1 in SMN2 exon 7. Finally, we propose a model for the assembly of multiple RNA binding proteins on this exon.

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Organizational Affiliation: 

Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zürich, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.42 kDa 
• Atom Count: 898 
• Modelled Residue Count: 101 
• Deposited Residue Count: 135 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transformer-2 protein homolog beta	B	129	Homo sapiens	Mutation(s): 0  Gene Names: TRA2B, SFRS10
UniProt & NIH Common Fund Data Resources
Find proteins for P62995 (Homo sapiens) Explore P62995  Go to UniProtKB:  P62995
PHAROS:  P62995

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*AP*AP*GP*AP*AP*C)-3'	A	6	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Clery, A., Jayne, S., Benderska, N., Dominguez, C., Stamm, S., Allain, F.H.-T.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-30
  Changes: Database references
• Version 1.3: 2020-02-05
  Changes: Data collection, Database references, Other