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 

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: 10.1261/rna.047209.114
  • Primary Citation of Related Structures:  

  • 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 RN ...

    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 cusack@embl.fr.,European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France.,Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211 Geneva 4, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
A
85Homo sapiensMutation(s): 0 
Gene Names: SRP9
Find proteins for P49458 (Homo sapiens)
Go to Gene View: SRP9
Go to UniProtKB:  P49458
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
B
107Homo sapiensMutation(s): 0 
Gene Names: SRP14
Find proteins for P37108 (Homo sapiens)
Go to Gene View: SRP14
Go to UniProtKB:  P37108
Entity ID: 3
MoleculeChainsLengthOrganism
SRP RNAR134Pyrococcus horikoshii OT3
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
R
RNA LINKINGC9 H13 N3 O10 P2C
MSE
Query on MSE
A, B
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 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.860α = 90.00
b = 100.860β = 90.00
c = 197.470γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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