8FLI | pdb_00008fli

Cryo-EM structure of a group II intron immediately before branching

• PDB DOI: https://doi.org/10.2210/pdb8FLI/pdb
• EM Map EMD-29279: EMDB EMDataResource
• NAKB: 8FLI

• Classification: SPLICING/RNA
• Organism(s): Thermosynechococcus vestitus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-12-21 Released: 2023-12-13 
• Deposition Author(s): Haack, D.B., Rudolfs, B.G., Zhang, C., Lyumkis, D., Toor, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of branching during RNA splicing.

Haack, D.B., Rudolfs, B., Zhang, C., Lyumkis, D., Toor, N.

(2024) Nat Struct Mol Biol 31: 179-189

• PubMed: 38057551 
• DOI: https://doi.org/10.1038/s41594-023-01150-0
• Primary Citation Related Structures: 
  8FLI


• PubMed Abstract: 
  

  Branching is a critical step in RNA splicing that is essential for 5' splice site selection. Recent spliceosome structures have led to competing models for the recognition of the invariant adenosine at the branch point. However, there are no structures of any splicing complex with the adenosine nucleophile docked in the active site and positioned to attack the 5' splice site. Thus we lack a mechanistic understanding of adenosine selection and splice site recognition during RNA splicing. Here we present a cryo-electron microscopy structure of a group II intron that reveals that active site dynamics are coupled to the formation of a base triple within the branch-site helix that positions the 2'-OH of the adenosine for nucleophilic attack on the 5' scissile phosphate. This structure, complemented with biochemistry and comparative analyses to splicing complexes, supports a base triple model of adenosine recognition for branching within group II introns and the evolutionarily related spliceosome.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
Salk Institute, La Jolla, CA, USA.
Amgen, Thousand Oaks, CA, USA.
Salk Institute, La Jolla, CA, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 354.4 kDa 
• Atom Count: 21,511 
• Modeled Residue Count: 1,286 
• Deposited Residue Count: 1,455 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maturase reverse transcriptase	B	562	Thermosynechococcus vestitus	Mutation(s): 1  Gene Names: tll0114
UniProt
Find proteins for Q8DMK2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DMK2  Go to UniProtKB:  Q8DMK2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Group II Intron	A	893	Thermosynechococcus vestitus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Haack, D.B., Rudolfs, B.G., Zhang, C., Lyumkis, D., Toor, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Database references