5M72

Structure of the human SRP68-72 protein-binding domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction.

Becker, M.M.Lapouge, K.Segnitz, B.Wild, K.Sinning, I.

(2017) Nucleic Acids Res. 45: 470-481

  • DOI: 10.1093/nar/gkw1124
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The tw ...

    Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP. The SRP72-PBD is a tetratricopeptide repeat, which binds an extended linear motif of SRP68 with high affinity. The SRP72-RBD is a flexible peptide crawling along the 5e- and 5f-loops of SRP RNA. A conserved tryptophan inserts into the 5e-loop forming a novel type of RNA kink-turn stabilized by a potassium ion, which we define as K+-turn. In addition, SRP72-RBD remodels the 5f-loop involved in ribosome binding and visualizes SRP RNA plasticity. Docking of the S domain structure into cryo-electron microscopy density maps reveals multiple contact sites between SRP68/72 and the ribosome, and explains the role of SRP72 in the SRP pathway.


    Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP72
A
160Homo sapiensMutation(s): 0 
Gene Names: SRP72
Find proteins for O76094 (Homo sapiens)
Go to Gene View: SRP72
Go to UniProtKB:  O76094
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP68
B
71Homo sapiensMutation(s): 0 
Gene Names: SRP68
Find proteins for Q9UHB9 (Homo sapiens)
Go to Gene View: SRP68
Go to UniProtKB:  Q9UHB9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.142 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.597α = 90.00
b = 52.269β = 118.22
c = 62.863γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanySFB 638
DFGGermanyGRK 1188

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2016-12-21
    Type: Database references
  • Version 1.3: 2017-01-18
    Type: Database references