2D3D

crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1

• PDB DOI: https://doi.org/10.2210/pdb2D3D/pdb

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


• Deposited: 2005-09-27 Released: 2006-02-14 
• Deposition Author(s): Aviv, T., Amborski, A.N., Zhao, X.S., Kwan, J.J., Johnson, P.E., Sicheri, F., Donaldson, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

The NMR and X-ray Structures of the Saccharomyces cerevisiae Vts1 SAM Domain Define a Surface for the Recognition of RNA Hairpins

Aviv, T., Amborski, A.N., Zhao, X.S., Kwan, J.J., Johnson, P.E., Sicheri, F., Donaldson, L.W.

(2006) J Mol Biol 356: 274-279

• PubMed: 16375924 
• DOI: https://doi.org/10.1016/j.jmb.2005.11.066
• Primary Citation of Related Structures:  
  2D3D


• PubMed Abstract: 
  

  The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1 has a high affinity towards RNA hairpins containing a CUGGC pentaloop. We present the 1.6 Angstroms X-ray crystal structure of the Vts1 SAM domain in its unliganded state, and the NMR solution structure of this domain in its RNA-bound state. Both structures reveal a canonical five helix SAM domain flanked by additional secondary structural elements at the N and C termini. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Amide chemical shift changes map the RNA-binding site to a shallow, basic patch at the junction of helix alpha5 and the loop connecting helices alpha1 and alpha2.

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Organizational Affiliation: 

Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ont., Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.12 kDa 
• Atom Count: 755 
• Modelled Residue Count: 83 
• Deposited Residue Count: 88 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vts1 protein	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.38	α = 90
b = 27.89	β = 90
c = 99.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Aviv, T., Amborski, A.N., Zhao, X.S., Kwan, J.J., Johnson, P.E., Sicheri, F., Donaldson, L.W.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations