9RIB | pdb_00009rib

Crystal structure of C278S mutant of mouse CDC14A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.210 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A truncated CDC14A retains catalytic structure and phosphatase activity preserving male fertility but causes nonsyndromic deafness.

Shabbir, K.Jackisch, G.Belyantseva, I.A.Imran, M.Naz, S.Sele, C.Murina, V.Knecht, W.Friedman, T.B.Logan, D.T.Imtiaz, A.

(2025) J Biological Chem 302: 110982-110982

  • DOI: https://doi.org/10.1016/j.jbc.2025.110982
  • Primary Citation of Related Structures:  
    9RIB, 9S1S

  • PubMed Abstract: 

    Pathogenic variants of human CDC14A (cell division cycle 14A) are associated either with nonsyndromic deafness DFNB32 or HIIMS, hearing impairment infertile male syndrome. The 623-residue CDC14A protein has two globular domains (residues 17-152 and 217-325) and a 278-residue C-terminal intrinsically disordered region (IDR). To date, 16 recessive variants of human CDC14A are associated with hearing loss. Variants affecting the globular N-terminal domains of human CDC14A are associated with HIIMS while mutations in the IDR cause nonsyndromic deafness DFNB32. Here, we tested the hypothesis that human CDC14A c.1033C>T variant, segregating with nonsyndromic deafness in family PKSN10, introduces a premature translation stop codon (p.R345X) yet the mRNA escapes nonsense-mediated decay (NMD) and produces sufficient active phosphatase to allow for male fertility. Quantitative analyses of CDC14A mRNA in blood leukocytes from PKSN10 family showed CDC14A transcripts are stable including homozygous (p.R345X) transcripts which evade NMD. To further test this hypothesis, we performed biochemical and structural characterizations of truncated CDC14A (ΔC-CDC14A) protein retaining only residues 1 to 345. Kinetic functional studies and X-ray crystallographic findings of purified ΔC-CDC14A protein indicate that it retains structural integrity and phosphatase activity. Molecular genetic reports of DFNB32 and HIIMS, taken together with structural and functional data in this study, indicate that phosphatase activity of ΔC-CDC14A containing the two globular domains is sufficient for male fertility but insufficient for normal hearing. In addition, we show that the C-terminal IDR of CDC14A is required for normal hearing, likely because it is necessary for normal localization of CDC14A in hair cells.


  • Organizational Affiliation
    • School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan; Section for Biochemistry and Structural Biology, Centre for Molecular Protein Science, Dept. of Chemistry, Lund University, Lund, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase CDC14A
A, B
344Mus musculusMutation(s): 1 
Gene Names: Cdc14a
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6GQT0 (Mus musculus)
Explore Q6GQT0 
Go to UniProtKB:  Q6GQT0
IMPC:  MGI:2442676
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GQT0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.507α = 90
b = 158.086β = 124.56
c = 69.156γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2023-05074

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references
  • Version 1.2: 2026-01-07
    Changes: Database references