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 

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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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEINA, D85Homo sapiensMutation(s): 1 
Gene Names: SRP9
UniProt & NIH Common Fund Data Resources
Find proteins for P49458 (Homo sapiens)
Explore P49458 
Go to UniProtKB:  P49458
PHAROS:  P49458
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49458
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEINB, E94Homo sapiensMutation(s): 3 
Gene Names: SRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P37108 (Homo sapiens)
Explore P37108 
Go to UniProtKB:  P37108
PHAROS:  P37108
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37108
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
ALU JO CONSENSUS RNAC, F87synthetic construct
Protein Feature View
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  • Reference Sequence
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

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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