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 5OBN | pdb_00005obn

NMR solution structure of U11/U12 65K protein's C-terminal RRM domain (381-516)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 5OBN

This is version 1.3 of the entry. See complete history. 

Literature

Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA.

Norppa, A.J., Kauppala, T.M., Heikkinen, H.A., Verma, B., Iwai, H., Frilander, M.J.

(2018) RNA 24: 396-409

  • DOI: https://doi.org/10.1261/rna.062844.117
  • Primary Citation Related Structures: 
    5OBN

  • PubMed Abstract: 

    Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbors mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs. We further show that the nonsense allele is targeted to the nonsense-mediated decay (NMD) pathway, but in an isoform-specific manner, with the nuclear-retained 65K long-3'UTR isoform escaping the NMD pathway. In contrast, the missense P474T mutation leads, in addition to the RNA-binding defect, to a partial defect in the folding of the C-RRM and reduced stability of the full-length protein, thus reducing the formation of U11/U12 di-snRNP complexes. We propose that both the C-RRM folding defect and NMD-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.


  • Organizational Affiliation: 
    • Institute of Biotechnology, FI-00014 University of Helsinki, Finland.

Macromolecule Content 

  • Total Structure Weight: 15.8 kDa 
  • Atom Count: 1,104 
  • Modeled Residue Count: 136 
  • Deposited Residue Count: 136 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 40136Homo sapiensMutation(s): 0 
Gene Names: RNPC3, KIAA1839, RBM40, RNP
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LT9 (Homo sapiens)
Explore Q96LT9 
Go to UniProtKB:  Q96LT9
PHAROS:  Q96LT9
GTEx:  ENSG00000185946 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LT9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland277335
Academy of FinlandFinland140087
Academy of FinlandFinland278798
Biocenter FinlandFinland--
Sigrid Juselius FoundationFinland--
Biocentrum HelsinkiFinland--
Integrative Life Science doctoral programFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references