Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.12 kDa 
• Atom Count: 1119 
• Modelled Residue Count: 100 
• Deposited Residue Count: 104 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2F8K

Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

• PDB DOI: 10.2210/pdb2F8K/pdb
• NDB: PR0186

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


• Deposited: 2005-12-02 Released: 2006-01-24 
• Deposition Author(s): Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C.A., Sicheri, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.

Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C.A., Sicheri, F.

(2006) Nat Struct Mol Biol 13: 168-176

• PubMed: 16429151 
• DOI: 10.1038/nsmb1053
• Primary Citation of Related Structures:  
  2F8K


• PubMed Abstract: 
  

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

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Organizational Affiliation: 

Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, M5G 1X5, Canada.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VTS1	B [auth A]	88	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*AP*AP*UP*CP*UP*UP*UP*GP*AP*CP*AP*GP*AP*UP*U)-3'	A [auth B]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.55	α = 90
b = 44.53	β = 90
c = 129.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-02 
• Released Date: 2006-01-24 
Deposition Author(s): Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C.A., Sicheri, F.

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: Advisory, Version format compliance