5IRF

Reverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P1 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.

Zhao, C.Pyle, A.M.

(2016) Nat.Struct.Mol.Biol. 23: 558-565

  • DOI: 10.1038/nsmb.3224
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection ...

    Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron-encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2-Å and 2.1-Å resolution, respectively. These domains are more similar in architecture to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron-maturase complexes.


    Organizational Affiliation

    Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retron-type reverse transcriptase
A, B, C, D
305Roseburia intestinalis XB6B4Mutation(s): 0 
Find proteins for D4L313 (Roseburia intestinalis XB6B4)
Go to UniProtKB:  D4L313
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.290α = 109.00
b = 79.160β = 90.56
c = 86.020γ = 105.04
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-03-13 
  • Released Date: 2016-05-04 
  • Deposition Author(s): Zhao, C., Pyle, A.M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1GM50313

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2016-06-22
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Type: Author supporting evidence