2B6G

RNA recognition by the Vts1 SAM domain

• PDB DOI: https://doi.org/10.2210/pdb2B6G/pdb
• BMRB: 6956
• NAKB: 2B6G

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


• Deposited: 2005-10-01 Released: 2006-01-24 
• Deposition Author(s): Donaldson, L.W., Johnson, P.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

RNA recognition by the Vts1p SAM domain

Johnson, P.E., Donaldson, L.W.

(2006) Nat Struct Mol Biol 13: 177-178

• PubMed: 16429155 
• DOI: https://doi.org/10.1038/nsmb1039
• Primary Citation of Related Structures:  
  2B6G, 2B7G


• PubMed Abstract: 
  

  The putative yeast post-transcriptional regulator Vts1p and its related protein Smaug, from Drosophila melanogaster, each use a sterile alpha motif (SAM) domain to bind an RNA hairpin termed the Smaug recognition element (SRE). Here, we present the NMR structures of the Vts1p-SRE complex and the free SRE. Structural highlights include the direct recognition of a guanine base and the formation or stabilization of a base pair in the SRE loop.

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Organizational Affiliation: 

Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario, Canada, M3J 1P3. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.18 kDa 
• Atom Count: 1,063 
• Modelled Residue Count: 100 
• Deposited Residue Count: 138 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vts1p	B [auth A]	119	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Vts1p
UniProt
Find proteins for Q08831 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08831  Go to UniProtKB:  Q08831

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3'	A [auth B]	19	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
RNA	PDBBind:  2B6G	Kd: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Donaldson, L.W., Johnson, P.E.

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: 2022-03-09
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection