Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 361.21 kDa 
• Atom Count: 21276 
• Modelled Residue Count: 1246 
• Deposited Residue Count: 1474 
• Unique protein chains: 1
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

6MEC

Structure of a group II intron retroelement after DNA integration

• PDB DOI: 10.2210/pdb6MEC/pdb
• EM Map EMD-9106: EMDB EMDataResource

• Classification: RNA/DNA/RNA Binding Protein
• Organism(s): Thermosynechococcus vestitus, Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-06 Released: 2019-08-14 
• Deposition Author(s): Haack, D., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., Toor, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.

Haack, D.B., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., Toor, N.

(2019) Cell 178: 612-623.e12

• PubMed: 31348888 
• DOI: 10.1016/j.cell.2019.06.035
• Primary Citation of Related Structures:  
  6ME0, 6MEC


• PubMed Abstract: 
  

Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-Å resolution of a group II intron reverse splicing into DNA. These structures reveal that the branch-site domain VI helix swings 90°, enabling substrate exchange during DNA integration. The maturase assists catalysis through a transient RNA-protein contact with domain VI that positions the branch-site adenosine for lariat formation during forward splicing. These findings provide the first direct evidence of the role the maturase plays during group II intron catalysis. The domain VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence for a retroelement origin of the spliceosome.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Maturase reverse transcriptase	C	562	Thermosynechococcus vestitus BP-1	Mutation(s): 0  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
T.el4h RNA	A	867	Thermosynechococcus vestitus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Sense Target DNA	B	45	Thermosynechococcus vestitus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	AA [auth A], AB [auth A], BA [auth A], CA [auth A], CB [auth C], 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], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	BB [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-06 
• Released Date: 2019-08-14 
Deposition Author(s): Haack, D., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., 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	1R01GM123275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM033050
National Institutes of Health/Office of the Director	United States	DP5 OD021396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54GM103368

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence