8QSW | pdb_00008qsw

Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.262 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.

Dharmadhikari, A.V.Abad, M.A.Khan, S.Maroofian, R.Sands, T.T.Ullah, F.Samejima, I.Shen, Y.Wear, M.A.Moore, K.E.Kondakova, E.Mitina, N.Schaub, T.Lee, G.K.Umandap, C.H.Berger, S.M.Iglesias, A.D.Popp, B.Abou Jamra, R.Gabriel, H.Rentas, S.Rippert, A.L.Gray, C.Izumi, K.Conlin, L.K.Koboldt, D.C.Mosher, T.M.Hickey, S.E.Albert, D.V.F.Norwood, H.Lewanda, A.F.Dai, H.Liu, P.Mitani, T.Marafi, D.Eker, H.K.Pehlivan, D.Posey, J.E.Lippa, N.C.Vena, N.Heinzen, E.L.Goldstein, D.B.Mignot, C.de Sainte Agathe, J.M.Al-Sannaa, N.A.Zamani, M.Sadeghian, S.Azizimalamiri, R.Seifia, T.Zaki, M.S.Abdel-Salam, G.M.H.Abdel-Hamid, M.S.Alabdi, L.Alkuraya, F.S.Dawoud, H.Lofty, A.Bauer, P.Zifarelli, G.Afzal, E.Zafar, F.Efthymiou, S.Gossett, D.Towne, M.C.Yeneabat, R.Perez-Duenas, B.Cazurro-Gutierrez, A.Verdura, E.Cantarin-Extremera, V.Marques, A.D.V.Helwak, A.Tollervey, D.Wontakal, S.N.Aggarwal, V.S.Rosenfeld, J.A.Tarabykin, V.Ohta, S.Lupski, J.R.Houlden, H.Earnshaw, W.C.Davis, E.E.Jeyaprakash, A.A.Liao, J.

(2025) Nat Commun 16: 1703-1703

  • DOI: https://doi.org/10.1038/s41467-025-56876-w
  • Primary Citation of Related Structures:  
    8QSU, 8QSV, 8QSW

  • PubMed Abstract: 

    SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.


  • Organizational Affiliation
    • Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative methyltransferase C9orf114307Homo sapiensMutation(s): 0 
Gene Names: SPOUT1
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T280 (Homo sapiens)
Explore Q5T280 
Go to UniProtKB:  Q5T280
PHAROS:  Q5T280
GTEx:  ENSG00000198917 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5T280
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.262 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.24α = 90
b = 80.694β = 90
c = 136.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/X001245/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Structure summary
  • Version 1.2: 2025-05-28
    Changes: Database references