6T3R | pdb_00006t3r

Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon

• PDB DOI: https://doi.org/10.2210/pdb6T3R/pdb
• NAKB: 6T3R

• Classification: RNA
• Organism(s): Oceanobacillus iheyensis HTE831, Oceanobacillus iheyensis
• Mutation(s): No 


• Deposited: 2019-10-11 Released: 2020-05-13 
• Deposition Author(s): Marcia, M., Pyle, A.M.
• Funding Organization(s): Other government, Howard Hughes Medical Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.57 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Visualizing group II intron dynamics between the first and second steps of splicing.

Manigrasso, J., Chillon, I., Genna, V., Vidossich, P., Somarowthu, S., Pyle, A.M., De Vivo, M., Marcia, M.

(2020) Nat Commun 11: 2837-2837

• PubMed: 32503992 
• DOI: https://doi.org/10.1038/s41467-020-16741-4
• Primary Citation Related Structures: 
  6T3K, 6T3N, 6T3R, 6T3S


• PubMed Abstract: 
  

  Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5'-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

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Organizational Affiliation: 
• Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
Department of Structural and Computational Biology, Institute for Research in Biomedicine (IRB), Parc Científic de Barcelona, C/ Baldiri Reixac 10-12, 08028, Barcelona, Spain.
Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA.
Department of Molecular, Cellular and Developmental Biology, New Haven, CT, 06511, USA.
Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy. [e-mail].
European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France. [e-mail].

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 132.25 kDa 
• Atom Count: 8,606 
• Modeled Residue Count: 394 
• Deposited Residue Count: 398 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Group IIC Intron Ribozyme	A	390	Oceanobacillus iheyensis HTE831

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Group IIC Intron Ribozyme	B	8	Oceanobacillus iheyensis

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	DB [auth A], EB [auth A], FB [auth A], WA [auth A], YA [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SPM	BB [auth A], CB [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
K	AB [auth A], BA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], XA [auth A], ZA [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [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 A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.57 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.458	α = 90
b = 95.1	β = 90
c = 222.402	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Marcia, M., Pyle, A.M.

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Funding Organization	Location	Grant Number
Other government	France	ANR-10-INSB-05-02
Other government	France	ANR-10-LABX-49-01
Howard Hughes Medical Institute	United States	--

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description