3KL4

Recognition of a signal peptide by the signal recognition particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.301 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recognition of a signal peptide by the signal recognition particle.

Janda, C.Y.Li, J.Oubridge, C.Hernandez, H.Robinson, C.V.Nagai, K.

(2010) Nature 465: 507-510

  • DOI: 10.1038/nature08870

  • PubMed Abstract: 
  • Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) whe ...

    Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP-ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP (refs 1, 2), SRP54 or its bacterial homologue, fifty-four homologue (Ffh), binds the signal peptides, which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8-20 hydrophobic residues and a polar c-region. No structure has been reported that exemplifies SRP54 binding of any signal sequence. Here we have produced a fusion protein between Sulfolobus solfataricus SRP54 (Ffh) and a signal peptide connected via a flexible linker. This fusion protein oligomerizes in solution through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, as demonstrated by its ability to bind SRP RNA and SRP receptor FtsY. We present the crystal structure at 3.5 A resolution of an SRP54-signal peptide complex in the dimer, which reveals how a signal sequence is recognized by SRP54.


    Related Citations: 
    • The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex.
      Montoya, G.,Kaat, K.,Moll, R.,Schafer, G.,Sinning, I.
      (2000) Structure 8: 515
    • Crystal structure of the ribonucleoprotein core of the signal recognition particle.
      Batey, R.T.,Rambo, R.P.,Lucast, L.,Rha, B.,Doudna, J.A.
      (2000) Science 287: 1232
    • Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
      Rosendal, K.R.,Wild, K.,Montoya, G.,Sinning, I.
      (2003) Proc.Natl.Acad.Sci.USA 100: 14701
    • Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
      Halic, M.,Blau, M.,Becker, T.,Mielke, T.,Pool, M.R.,Wild, K.,Sinning, I.,Beckmann, R.
      (2006) Nature 444: 507
    • Crystal structure of the signal sequence binding subunit of the signal recognition particle.
      Keenan, R.J.,Freymann, D.M.,Walter, P.,Stroud, R.M.
      (1998) Cell 94: 181


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Signal recognition 54 kDa protein
A
433Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: srp54
Find proteins for Q97ZE7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97ZE7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Signal peptide of yeast dipeptidyl aminopeptidase B
B
42Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DAP2
EC: 3.4.14.-
Find proteins for P18962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P18962
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.301 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.883α = 90.00
b = 91.883β = 90.00
c = 133.263γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MxCuBEdata collection
SCALAdata scaling
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations