4ZC4

Crystal structure of LARP1-unique domain DM15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.

Lahr, R.M.Mack, S.M.Heroux, A.Blagden, S.P.Bousquet-Antonelli, C.Deragon, J.M.Berman, A.J.

(2015) Nucleic Acids Res. 43: 8077-8088

  • DOI: 10.1093/nar/gkv748
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP ...

    La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.


    Related Citations: 
    • The LARP1-specific domain DM15 repurposes HEAT-like repeats to directly bind messenger RNA
      Lahr, R.M.,Mack, S.M.,Heroux, A.,Blagden, S.P.,Bousquet-Antonelli, C.,Deragon, J.M.,Berman, A.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
La-related protein 1
A, B, C, D
162Homo sapiensMutation(s): 0 
Gene Names: LARP1 (KIAA0731, LARP)
Find proteins for Q6PKG0 (Homo sapiens)
Go to Gene View: LARP1
Go to UniProtKB:  Q6PKG0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.906α = 90.00
b = 61.759β = 116.20
c = 85.336γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references