7QDE | pdb_00007qde

NMR structure of Npl3 RRM12 bound to the AUCCAGUGGAA RNA

• PDB DOI: https://doi.org/10.2210/pdb7QDE/pdb
• BMRB: 34692
• NAKB: 7QDE

• Classification: RNA BINDING PROTEIN
• Organism(s): synthetic construct, Saccharomyces cerevisiae S288C
• Expression System: unidentified plasmid
• Mutation(s): No 


• Deposited: 2021-11-26 Released: 2022-12-21 
• Deposition Author(s): Allain, F.H.-T., Clery, A., Moursy, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing.

Moursy, A., Clery, A., Gerhardy, S., Betz, K.M., Rao, S., Mazur, J., Campagne, S., Beusch, I., Duszczyk, M.M., Robinson, M.D., Panse, V.G., Allain, F.H.

(2023) Nat Commun 14: 7166-7166

• PubMed: 37935663 
• DOI: https://doi.org/10.1038/s41467-023-42962-4
• Primary Citation Related Structures: 
  7QDD, 7QDE


• PubMed Abstract: 
  

  The conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in yeast to uncover the consensus sequence bound to each RRM. High-resolution NMR structures show that RRM2 recognizes a 5´-GNGG-3´ motif leading to an unusual mille-feuille topology. These structures also reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contribute to cooperative RNA-binding. Structure-guided functional studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic center of the B ^act spliceosomal complex. Thus, our findings suggest an unanticipated RNA chaperoning role for Npl3 during spliceosome active site formation.

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Organizational Affiliation: 
• Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland.
Novartis Institutes for BioMedical Research, Basel, Switzerland.
Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland. [e-mail].
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
Sardona Therapeutics, San Francisco, CA, USA.
Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
ARNA laboratory, INSERM U1212, University of Bordeaux, Bordeaux, France.
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland. [e-mail].
Faculty of Science, University of Zurich, Zurich, Switzerland. [e-mail].
Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland. [e-mail].

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: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 22.82 kDa 
• Atom Count: 1,593 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 3	B	169	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NPL3, MTR13, MTS1, NAB1, NOP3, YDR432W, D9461.19
UniProt
Find proteins for Q01560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01560  Go to UniProtKB:  Q01560

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*UP*CP*CP*AP*GP*UP*GP*GP*AP*A)-3')	A	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Allain, F.H.-T., Clery, A., Moursy, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B-189379

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references