5G2X | pdb_00005g2x

Structure a of Group II Intron Complexed with its Reverse Transcriptase


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of a Group II Intron in Complex with its Reverse Transcriptase.

Qu, G.Kaushal, P.S.Wang, J.Shigematsu, H.Piazza, C.L.Agrawal, R.K.Belfort, M.Wang, H.

(2016) Nat Struct Mol Biol 23: 549

  • DOI: https://doi.org/10.1038/nsmb.3220
  • Primary Citation Related Structures: 
    5G2X, 5G2Y

  • PubMed Abstract: 

    Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.


  • Organizational Affiliation
    • Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 301.65 kDa 
  • Atom Count: 19,072 
  • Modeled Residue Count: 1,191 
  • Deposited Residue Count: 1,315 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GROUP II INTRON-ENCODED PROTEIN LTRA599Lactococcus cremorisMutation(s): 0 
Gene Names: LTRAMATR
EC: 2.7.7.49 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P0A3U0 (Lactococcus lactis subsp. cremoris)
Explore P0A3U0 
Go to UniProtKB:  P0A3U0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3U0
Sequence Annotations
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
GROUP II INTRON704Lactococcus lactis
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*CP)-3'12Lactococcus cremoris
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations