6PW3

LARP1 DM15 FYRE (F844Y, R847E) mutant bound to m7GpppG dinucleotide (capG)

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-07-22 Released: 2019-11-06 
  • Deposition Author(s): Lahr, R.M., Berman, A.J.
  • Funding Organization(s): American Cancer Society, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Capturing the Mechanism Underlying TOP mRNA Binding to LARP1.

Cassidy, K.C.Lahr, R.M.Kaminsky, J.C.Mack, S.Fonseca, B.D.Das, S.R.Berman, A.J.Durrant, J.D.

(2019) Structure 27: 1771

  • DOI: 10.1016/j.str.2019.10.006
  • Primary Citation of Related Structures:  
    6PW3

  • PubMed Abstract: 
  • The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m 7 G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors ...

    The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m 7 G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m 7 G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m 7 GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.


    Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA. Electronic address: durrantj@pitt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
La-related protein 1B [auth A],
C [auth B],
A [auth C],
D
162Homo sapiensMutation(s): 2 
Gene Names: LARP1KIAA0731LARP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PKG0 (Homo sapiens)
Explore Q6PKG0 
Go to UniProtKB:  Q6PKG0
PHAROS:  Q6PKG0
GTEx:  ENSG00000155506 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PKG0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTG (Subject of Investigation/LOI)
Query on GTG

Download Ideal Coordinates CCD File 
E [auth C],
G [auth B]
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.582α = 90
b = 87.355β = 93.367
c = 72.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Cancer Society--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence