Biological Assembly 1  

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Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 5266.17 
• Atom Count: 346 
• Residue Count: 16 
• Unique nucleic acid chains: 1

3D0M

X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex

• DOI: 10.2210/pdb3D0M/pdb
• NDB: AR0099

• Classification: RNA


• Deposited: 2008-05-02 Released: 2008-09-09 
• Deposition Author(s): Rypniewski, W., Adamiak, D.A., Milecki, J., Adamiak, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.361 
• R-Value Work: 0.295 

Literature

Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.

Rypniewski, W., Adamiak, D.A., Milecki, J., Adamiak, R.W.

(2008) Rna 14: 1845-1851

• PubMed: 18658118 
• DOI: 10.1261/rna.1164308
• Primary Citation of Related Structures:  
  3CZW


• PubMed Abstract: 
  

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań , Poland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
RNA (5'-R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3')	X	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	X	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.361 
• R-Value Work: 0.295 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 46.653	α = 90.00
b = 46.653	β = 90.00
c = 126.397	γ = 120.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-02 
• Released Date: 2008-09-09 
• Deposition Author(s): Rypniewski, W., Adamiak, D.A., Milecki, J., Adamiak, R.W.

Revision History 

• Version 1.0: 2008-09-09
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description