2FE9 | pdb_00002fe9

Solution structure of the Vts1 SAM domain in the presence of RNA

• PDB DOI: https://doi.org/10.2210/pdb2FE9/pdb
• BMRB: 6922

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-15 Released: 2006-01-24 
• Deposition Author(s): Edwards, T.A., Butterwick, J.A., Palmer, A.G., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution Structure of the Vts1 SAM Domain in the Presence of RNA.

Edwards, T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X., Wharton, R.P., Palmer, A.G., Aggarwal, A.K.

(2006) J Mol Biology 356: 1065-1072

• PubMed: 16405996 
• DOI: https://doi.org/10.1016/j.jmb.2005.12.004
• Primary Citation Related Structures: 
  2FE9


• PubMed Abstract: 
  

  The yeast Vts1 SAM (sterile alpha motif) domain is a member of a new class of SAM domains that specifically bind RNA. To elucidate the structural basis for RNA binding, the solution structure of the Vts1 SAM domain, in the presence of a specific target RNA, has been solved by multidimensional heteronuclear NMR spectroscopy. The Vts1 SAM domain retains the "core" five-helix-bundle architecture of traditional SAM domains, but has additional short helices at N and C termini, comprising a small substructure that caps the core helices. The RNA-binding surface of Vts1, determined by chemical shift perturbation, maps near the ends of three of the core helices, in agreement with mutational data and the electrostatic properties of the molecule. These results provide a structural basis for the versatility of the SAM domain in protein and RNA-recognition.

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Organizational Affiliation: 
• Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.88 kDa 
• Atom Count: 695 
• Modeled Residue Count: 86 
• Deposited Residue Count: 86 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VTS1	A	86	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: VTS1
UniProt
Find proteins for Q08831 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08831  Go to UniProtKB:  Q08831

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Edwards, T.A., Butterwick, J.A., Palmer, A.G., Aggarwal, A.K.

Revision History  

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-02-05
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2023-06-14
  Changes: Database references, Other
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references