Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.25 kDa 
• Atom Count: 568 
• Residue Count: 26 
• Unique nucleic acid chains: 1

1I9X

CRYSTAL STRUCTURE OF BPS-U2 SNRNA DUPLEX

• DOI: 10.2210/pdb1I9X/pdb
• NDB: AR0032

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-03-21 Released: 2001-09-05 
• Deposition Author(s): Berglund, J.A., Rosbash, M., Schultz, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.276 
• R-Value Work: 0.253 

Literature

Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines.

Berglund, J.A., Rosbash, M., Schultz, S.C.

(2001) RNA 7: 682-691

• PubMed: 11350032 
• DOI: 10.1017/s1355838201002187
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Bulged nucleotides play a variety of important roles in RNA structure and function, frequently forming tertiary interactions and sometimes even participating in RNA catalysis. In pre-mRNA splicing, the U2 snRNA base pairs with the intron branchpoint sequence (BPS) to form a short RNA duplex that contains a bulged adenosine that ultimately serves as the nucleophile that attacks the 5' splice site. We have determined a 2.18-A resolution crystal structure of a self-complementary RNA designed to mimic the highly conserved yeast (Saccharomyces cerevisiae) branchpoint sequence (5'-UACUAACGUAGUA with the BPS italicized and the branchsite adenosine underlined) base paired with its complementary sequence from U2 snRNA. The structure shows a nearly ideal A-form helix from which two unpaired adenosines flip out. Although the adenosine adjacent to the branchsite adenosine is the one bulged out in the structure described here, either of these adenosines can serve as the nucleophile in mammalian but not in yeast pre-mRNA splicing. In addition, the packing of the bulged RNA helices within the crystal reveals a novel RNA tertiary interaction in which three RNA helices interact through bulged adenosines in the absence of any divalent metal ions.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3'	A, B	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.276 
• R-Value Work: 0.253 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.75	α = 90
b = 42.4	β = 92.87
c = 33.14	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-21 
• Released Date: 2001-09-05 
Deposition Author(s): Berglund, J.A., Rosbash, M., Schultz, S.C.

Revision History 

• Version 1.0: 2001-09-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection