6MEC

Structure of a group II intron retroelement after DNA integration


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1016/j.cell.2019.06.035
  • Primary Citation of Related Structures:  

  • 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 unk ...

    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.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: tsb@ucsd.edu.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.,Salk Institute, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: ntoor@ucsd.edu.,Salk Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Maturase reverse transcriptase
C
562Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Find proteins for Q8DMK2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DMK2
Entity ID: 1
MoleculeChainsLengthOrganism
T.el4h RNAA867Thermosynechococcus elongatus
Entity ID: 2
MoleculeChainsLengthOrganism
Sense Target DNAB45Thermosynechococcus elongatus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
phenix.real_space_refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM123275
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM033050
National Institutes of Health/Office of the DirectorUnited StatesDP5 OD021396
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54GM103368

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release