7SOQ

LaM domain of human LARP1 in complex with AAA RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of 3'-end poly(A) RNA recognition by LARP1.

Kozlov, G., Mattijssen, S., Jiang, J., Nyandwi, S., Sprules, T., Iben, J.R., Coon, S.L., Gaidamakov, S., Noronha, A.M., Wilds, C.J., Maraia, R.J., Gehring, K.

(2022) Nucleic Acids Res 50: 9534-9547

  • DOI: https://doi.org/10.1093/nar/gkac696
  • Primary Citation of Related Structures:  
    7SOO, 7SOP, 7SOQ, 7SOR, 7SOS, 7SOT, 7SOU, 7SOV

  • PubMed Abstract: 

    • La-related proteins (LARPs) comprise a family of RNA-binding proteins involved in a wide range of posttranscriptional regulatory activities. LARPs share a unique tandem of two RNA-binding domains, La motif (LaM) and RNA recognition motif (RRM), together referred to as a La-module, but vary in member-specific regions ...

    La-related proteins (LARPs) comprise a family of RNA-binding proteins involved in a wide range of posttranscriptional regulatory activities. LARPs share a unique tandem of two RNA-binding domains, La motif (LaM) and RNA recognition motif (RRM), together referred to as a La-module, but vary in member-specific regions. Prior structural studies of La-modules reveal they are pliable platforms for RNA recognition in diverse contexts. Here, we characterize the La-module of LARP1, which plays an important role in regulating synthesis of ribosomal proteins in response to mTOR signaling and mRNA stabilization. LARP1 has been well characterized functionally but no structural information exists for its La-module. We show that unlike other LARPs, the La-module in LARP1 does not contain an RRM domain. The LaM alone is sufficient for binding poly(A) RNA with submicromolar affinity and specificity. Multiple high-resolution crystal structures of the LARP1 LaM domain in complex with poly(A) show that it is highly specific for the RNA 3'-end, and identify LaM residues Q333, Y336 and F348 as the most critical for binding. Use of a quantitative mRNA stabilization assay and poly(A) tail-sequencing demonstrate functional relevance of LARP1 RNA binding in cells and provide novel insight into its poly(A) 3' protection activity.

    Organizational Affiliation: 

    Centre de recherche en biologie structurale, McGill University, Montréal, Canada.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of La-related protein 1A99Homo sapiensMutation(s): 0 
Gene Names: LARP1, KIAA0731, LARP
UniProt
Find proteins for Q6PKG0-3 (Homo sapiens)
Explore Q6PKG0-3 
Go to UniProtKB:  Q6PKG0-3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PKG0-3
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*AP*A)-3')B3synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.915α = 90
b = 46.474β = 90
c = 59.135γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references