2N82 | pdb_00002n82

solution structure of the complex of microRNA 20b pre-element with Rbfox RRM

• PDB DOI: https://doi.org/10.2210/pdb2N82/pdb
• NAKB: 2N82
• BMRB: 25831

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


• Deposited: 2015-09-30 Released: 2016-04-13 
• Deposition Author(s): Yang, F., Chen, Y., Varani, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer.

Chen, Y., Zubovic, L., Yang, F., Godin, K., Pavelitz, T., Castellanos, J., Macchi, P., Varani, G.

(2016) Nucleic Acids Res 44: 4381-4395

• PubMed: 27001519 
• DOI: https://doi.org/10.1093/nar/gkw177
• Primary Citation Related Structures: 
  2N7X, 2N82


• PubMed Abstract: 
  

  Rbfox proteins regulate tissue-specific splicing by targeting a conserved GCAUG sequence within pre-mRNAs. We report here that sequence-specific binding of the conserved Rbfox RRM to miRNA precursors containing the same sequence motif in their terminal loops, including miR-20b and miR-107, suppresses their nuclear processing. The structure of the complex between precursor miR-20b and Rbfox RRM shows the molecular basis for recognition, and reveals changes in the stem-loop upon protein binding. In mammalian cells, Rbfox2 downregulates mature miR-20b and miR-107 levels and increases the expression of their downstream targets PTEN and Dicer, respectively, suggesting that Rbfox2 indirectly regulates many more cellular miRNAs. Thus, some of the widespread cellular functions of Rbfox2 protein are attributable to regulation of miRNA biogenesis, and might include the mis-regulation of miR-20b and miR-107 in cancer and neurodegeneration.

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Organizational Affiliation: 
• Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy.
Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.
Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA [e-mail].
Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 19.15 kDa 
• Atom Count: 1,315 
• Modeled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA binding protein fox-1 homolog 1	B	104	Homo sapiens	Mutation(s): 0  Gene Names: RBFOX1, A2BP, A2BP1, FOX1, HRNBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWB1 (Homo sapiens) Explore Q9NWB1  Go to UniProtKB:  Q9NWB1
PHAROS:  Q9NWB1 GTEx:  ENSG00000078328

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')	A	23	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Yang, F., Chen, Y., Varani, G.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references