8EY8 | pdb_00008ey8

LaM domain of human LARP1 in complex with AAAAGA RNA

• PDB DOI: https://doi.org/10.2210/pdb8EY8/pdb
• NAKB: 8EY8

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-26 Released: 2023-11-01 
• Deposition Author(s): Kozlov, G., Gehring, K.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Enhanced binding of guanylated poly(A) RNA by the LaM domain of LARP1.

Kozlov, G., Jiang, J., Rutherford, T., Noronha, A.M., Wilds, C.J., Gehring, K.

(2024) RNA Biol 21: 7-16

• PubMed: 39016322 
• DOI: https://doi.org/10.1080/15476286.2024.2379121
• Primary Citation Related Structures: 
  7SOW, 8EY6, 8EY7, 8EY8, 8G90, 8G91


• PubMed Abstract: 
  

  La-related proteins (LARPs) are a family of RNA-binding proteins that share a conserved La motif (LaM) domain. LARP1 plays a role in regulating ribosomal protein synthesis and stabilizing mRNAs and has a unique structure without an RNA binding RRM domain adjoining the LaM domain. In this study, we investigated the physical basis for LARP1 specificity for poly(A) sequences and observed an unexpected bias for sequences with single guanines. Multiple guanine substitutions did not increase the affinity, demonstrating preferential recognition of singly guanylated sequences. We also observed that the cyclic di-nucleotides in the cCAS/STING pathway, cyclic-di-GMP and 3',3'-cGAMP, bound with sub-micromolar affinity. Isothermal titration measurements were complemented by high-resolution crystal structures of the LARP1 LaM with six different RNA ligands, including two stereoisomers of a phosphorothioate linkage. The selectivity for singly substituted poly(A) sequences suggests LARP1 may play a role in the stabilizing effect of poly(A) tail guanylation. [Figure: see text].

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montréal, Quebec, Canada.
Centre de recherche en biologie structurale, McGill University, Montréal, Quebec, Canada.
Department of Chemistry and Biochemistry, Concordia University, Montréal, Quebec, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 13.75 kDa 
• Atom Count: 885 
• Modeled Residue Count: 92 
• Deposited Residue Count: 105 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of La-related protein 1	A	99	Homo sapiens	Mutation(s): 0  Gene Names: LARP1, KIAA0731, LARP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PKG0 (Homo sapiens) Explore Q6PKG0  Go to UniProtKB:  Q6PKG0
PHAROS:  Q6PKG0 GTEx:  ENSG00000155506

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*AP*AP*GP*A)-3')	B	6	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.683	α = 90
b = 45.879	β = 90
c = 58.861	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Kozlov, G., Gehring, K.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Database references, Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description