6MEC

Structure of a group II intron retroelement after DNA integration


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    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 ...

    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. Electronic address: ntoor@ucsd.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Maturase reverse transcriptaseC562Thermosynechococcus vestitus BP-1Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DMK2
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
T.el4h RNAA 867Thermosynechococcus vestitus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Sense Target DNAB 45Thermosynechococcus vestitus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
BA [auth A],
CA [auth A],
CB [auth C],
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
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BB [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM123275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM033050
National Institutes of Health/Office of the DirectorUnited StatesDP5 OD021396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM103368

Revision History  (Full details and data files)

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