5OR0 | pdb_00005or0

NMR derived model of the 5'-splice site of SMN2 in complex with the 5'-end of U1 snRNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers.

Sivaramakrishnan, M.McCarthy, K.D.Campagne, S.Huber, S.Meier, S.Augustin, A.Heckel, T.Meistermann, H.Hug, M.N.Birrer, P.Moursy, A.Khawaja, S.Schmucki, R.Berntenis, N.Giroud, N.Golling, S.Tzouros, M.Banfai, B.Duran-Pacheco, G.Lamerz, J.Hsiu Liu, Y.Luebbers, T.Ratni, H.Ebeling, M.Clery, A.Paushkin, S.Krainer, A.R.Allain, F.H.Metzger, F.

(2017) Nat Commun 8: 1476-1476

  • DOI: https://doi.org/10.1038/s41467-017-01559-4
  • Primary Citation Related Structures: 
    5OR0

  • PubMed Abstract: 

    Small molecule splicing modifiers have been previously described that target the general splicing machinery and thus have low specificity for individual genes. Several potent molecules correcting the splicing deficit of the SMN2 (survival of motor neuron 2) gene have been identified and these molecules are moving towards a potential therapy for spinal muscular atrophy (SMA). Here by using a combination of RNA splicing, transcription, and protein chemistry techniques, we show that these molecules directly bind to two distinct sites of the SMN2 pre-mRNA, thereby stabilizing a yet unidentified ribonucleoprotein (RNP) complex that is critical to the specificity of these small molecules for SMN2 over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work has wide-ranging implications in understanding how small molecules can interact with specific quaternary RNA structures.


  • Organizational Affiliation
    • F. Hoffmann-La Roche Ltd., Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel, 4070, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 6.98 kDa 
  • Atom Count: 467 
  • Modeled Residue Count: 22 
  • Deposited Residue Count: 22 
  • Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3')11Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3')11Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-06-19
    Changes: Data collection, Database references