4P3E

Structure of the human SRP S domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

SRP RNA remodeling by SRP68 explains its role in protein translocation.

Grotwinkel, J.T.Wild, K.Segnitz, B.Sinning, I.

(2014) Science 344: 101-104

  • DOI: 10.1126/science.1249094
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The signal recognition particle (SRP) is central to membrane protein targeting; SRP RNA is essential for SRP assembly, elongation arrest, and activation of SRP guanosine triphosphatases. In eukaryotes, SRP function relies on the SRP68-SRP72 heterodim ...

    The signal recognition particle (SRP) is central to membrane protein targeting; SRP RNA is essential for SRP assembly, elongation arrest, and activation of SRP guanosine triphosphatases. In eukaryotes, SRP function relies on the SRP68-SRP72 heterodimer. We present the crystal structures of the RNA-binding domain of SRP68 (SRP68-RBD) alone and in complex with SRP RNA and SRP19. SRP68-RBD is a tetratricopeptide-like module that binds to a RNA three-way junction, bends the RNA, and inserts an α-helical arginine-rich motif (ARM) into the major groove. The ARM opens the conserved 5f RNA loop, which in ribosome-bound SRP establishes a contact to ribosomal RNA. Our data provide the structural basis for eukaryote-specific, SRP68-driven RNA remodeling required for protein translocation.


    Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 19 kDa protein
B
128Homo sapiensMutation(s): 0 
Gene Names: SRP19
Find proteins for P09132 (Homo sapiens)
Go to Gene View: SRP19
Go to UniProtKB:  P09132
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP68
C
216Homo sapiensMutation(s): 1 
Gene Names: SRP68
Find proteins for Q9UHB9 (Homo sapiens)
Go to Gene View: SRP68
Go to UniProtKB:  Q9UHB9
Entity ID: 1
MoleculeChainsLengthOrganism
SRP RNA (124-mer)A125Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.649α = 90.00
b = 70.530β = 100.46
c = 106.493γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB638

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Data collection
  • Version 1.2: 2014-07-09
    Type: Structure summary
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary