7Q33 | pdb_00007q33

Solution structure of RBM39 RRM2 bound to 5'-AGCUUUG-3

• PDB DOI: https://doi.org/10.2210/pdb7Q33/pdb
• NAKB: 7Q33
• BMRB: 34673

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, synthetic construct
• Mutation(s): No 


• Deposited: 2021-10-26 Released: 2023-02-08 
• Deposition Author(s): Campagne, S., Allain, F.H.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.

Campagne, S., Jutzi, D., Malard, F., Matoga, M., Romane, K., Feldmuller, M., Colombo, M., Ruepp, M.D., Allain, F.H.

(2023) Nat Commun 14: 5366-5366

• PubMed: 37666821 
• DOI: https://doi.org/10.1038/s41467-023-40254-5
• Primary Citation Related Structures: 
  7Q33, 7ZAP


• PubMed Abstract: 
  

  Pharmacologic depletion of RNA-binding motif 39 (RBM39) using aryl sulfonamides represents a promising anti-cancer therapy but requires high levels of the adaptor protein DCAF15. Consequently, novel approaches to deplete RBM39 in an DCAF15-independent manner are required. Here, we uncover that RBM39 autoregulates via the inclusion of a poison exon into its own pre-mRNA and identify the cis-acting elements that govern this regulation. We also determine the NMR solution structures of RBM39's tandem RNA recognition motifs (RRM1 and RRM2) bound to their respective RNA targets, revealing how RRM1 recognises RNA stem loops whereas RRM2 binds specifically to single-stranded N(G/U)NUUUG. Our results support a model where RRM2 selects the 3'-splice site of a poison exon and the RRM3 and RS domain stabilise the U2 snRNP at the branchpoint. Our work provides molecular insights into RBM39-dependent 3'-splice site selection and constitutes a solid basis to design alternative anti-cancer therapies.

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Organizational Affiliation: 
• ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland. [e-mail].
University of Bordeaux, Inserm U1212, CNRS UMR5320, ARNA Laboratory, 33077, Bordeaux, France. [e-mail].
United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9NU, UK.
ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland.
University of Bordeaux, Inserm U1212, CNRS UMR5320, ARNA Laboratory, 33077, Bordeaux, France.
University of Bern, Department of Chemistry and Biochemistry, 3012, Bern, Switzerland.
Celgene Institute of Translational Research in Europe (CITRE), Bristol Myers Squibb, 41092, Seville, Spain.
United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9NU, UK. [e-mail].
ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 12.64 kDa 
• Atom Count: 873 
• Modeled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 39	A	93	Homo sapiens	Mutation(s): 0  Gene Names: RBM39, HCC1, RNPC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14498 (Homo sapiens) Explore Q14498  Go to UniProtKB:  Q14498
PHAROS:  Q14498 GTEx:  ENSG00000131051

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*GP*CP*UP*UP*UP*G)-3')	B	7	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Campagne, S., Allain, F.H.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	NCCR RNA and Diseases

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references
• Version 1.2: 2023-09-20
  Changes: Database references