4UYK

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.

Bousset, L.Mary, C.Brooks, M.A.Scherrer, A.Strub, K.Cusack, S.

(2014) RNA 20: 1955

  • DOI: https://doi.org/10.1261/rna.047209.114
  • Primary Citation of Related Structures:  
    4UYJ, 4UYK

  • PubMed Abstract: 

    The signal recognition particle (SRP) is a conserved ribonucleoprotein particle that targets membrane and secreted proteins to translocation channels in membranes. In eukaryotes, the Alu domain, which comprises the 5' and 3' extremities of the SRP RNA bound to the SRP9/14 heterodimer, is thought to interact with the ribosome to pause translation elongation during membrane docking. We present the 3.2 Å resolution crystal structure of a chimeric Alu domain, comprising Alu RNA from the archaeon Pyrococcus horikoshii bound to the human Alu binding proteins SRP9/14. The structure reveals how intricate tertiary interactions stabilize the RNA 5' domain structure and how an extra, archaeal-specific, terminal stem helps constrain the Alu RNA into the active closed conformation. In this conformation, highly conserved noncanonical base pairs allow unusually tight side-by-side packing of 5' and 3' RNA stems within the SRP9/14 RNA binding surface. The biological relevance of this structure is confirmed by showing that a reconstituted full-length chimeric archaeal-human SRP is competent to elicit elongation arrest in vitro. The structure will be useful in refining our understanding of how the SRP Alu domain interacts with the ribosome.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN85Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49458 (Homo sapiens)
Explore P49458 
Go to UniProtKB:  P49458
PHAROS:  P49458
GTEx:  ENSG00000143742 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49458
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN107Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P37108 (Homo sapiens)
Explore P37108 
Go to UniProtKB:  P37108
PHAROS:  P37108
GTEx:  ENSG00000140319 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37108
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
SRP RNAC [auth R]134Pyrococcus horikoshii OT3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.86α = 90
b = 100.86β = 90
c = 197.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references