3GS1

An all-RNA Hairpin Ribozyme with mutation A38N1dA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of an imino group indispensable for cleavage by a small ribozyme.

Spitale, R.C.Volpini, R.Heller, M.G.Krucinska, J.Cristalli, G.Wedekind, J.E.

(2009) J Am Chem Soc 131: 6093-6095

  • DOI: 10.1021/ja900450h
  • Primary Citation of Related Structures:  
    3GS1, 3GS5, 3GS8

  • PubMed Abstract: 
  • The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site ...

    The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')A14N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3')B12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')C17N/A
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')D19N/A
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S9L
Query on S9L

Download Ideal Coordinates CCD File 
G [auth C]2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE
C6 H15 O7 P
CJHGCXGTUHBMMH-UHFFFAOYSA-N
 Ligand Interaction
NCO
Query on NCO

Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.79α = 90
b = 93.79β = 90
c = 130.08γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance