5AOX

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Retrotransposition and Crystal Structure of an Alu Rnp in the Ribosome-Stalling Conformation.

Ahl, V.Keller, H.Schmidt, S.Weichenrieder, O.

(2015) Mol Cell 60: 715

  • DOI: 10.1016/j.molcel.2015.10.003
  • Primary Citation of Related Structures:  
    5AOX

  • PubMed Abstract: 
  • The Alu element is the most successful human genomic parasite affecting development and causing disease. It originated as a retrotransposon during early primate evolution of the gene encoding the signal recognition particle (SRP) RNA. We defined a minimal Alu RNA sufficient for effective retrotransposition and determined a high-resolution structure of its complex with the SRP9/14 proteins ...

    The Alu element is the most successful human genomic parasite affecting development and causing disease. It originated as a retrotransposon during early primate evolution of the gene encoding the signal recognition particle (SRP) RNA. We defined a minimal Alu RNA sufficient for effective retrotransposition and determined a high-resolution structure of its complex with the SRP9/14 proteins. The RNA adopts a compact, closed conformation that matches the envelope of the SRP Alu domain in the ribosomal translation elongation factor-binding site. Conserved structural elements in SRP RNAs support an ancient function of the closed conformation that predates SRP9/14. Structure-based mutagenesis shows that retrotransposition requires the closed conformation of the Alu ribonucleoprotein particle and is consistent with the recognition of stalled ribosomes. We propose that ribosome stalling is a common cause for the cis-preference of the mammalian L1 retrotransposon and for the efficiency of the Alu RNA in hijacking nascent L1 reverse transcriptase.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany. Electronic address: oliver.weichenrieder@tuebingen.mpg.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN AD85Homo sapiensMutation(s): 1 
Gene Names: SRP9
Find proteins for P49458 (Homo sapiens)
Explore P49458 
Go to UniProtKB:  P49458
NIH Common Fund Data Resources
PHAROS:  P49458
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN BE94Homo sapiensMutation(s): 3 
Gene Names: SRP14
Find proteins for P37108 (Homo sapiens)
Explore P37108 
Go to UniProtKB:  P37108
NIH Common Fund Data Resources
PHAROS:  P37108
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
ALU JO CONSENSUS RNAC, F87synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.48α = 90
b = 56.73β = 93.69
c = 170.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Derived calculations, Other