6UFK

Pistol ribozyme product crystal soaked in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme.

Teplova, M.Falschlunger, C.Krasheninina, O.Egger, M.Ren, A.Patel, D.J.Micura, R.

(2020) Angew Chem Int Ed Engl 59: 2837-2843

  • DOI: https://doi.org/10.1002/anie.201912522
  • Primary Citation of Related Structures:  
    6UEY, 6UF1, 6UFJ, 6UFK

  • PubMed Abstract: 

    Pistol ribozymes constitute a new class of small self-cleaving RNAs. Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg 2+ ion remains innersphere-coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg 2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg 2+ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA.


Macromolecules
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (50-MER)A,
D [auth C]
51synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')B,
E [auth D]
10synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*CP*CP*AP*G)-3')C [auth E],
F
5synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth F]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
BA [auth F],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth E],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.346α = 90
b = 90.346β = 90
c = 121.732γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Source and taxonomy
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations