8OU1

Crystal structure of the SPOC domain of mouse SPOCD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line.

Zoch, A.Konieczny, G.Auchynnikava, T.Stallmeyer, B.Rotte, N.Heep, M.Berrens, R.V.Schito, M.Kabayama, Y.Schopp, T.Kliesch, S.Houston, B.Nagirnaja, L.O'Bryan, M.K.Aston, K.I.Conrad, D.F.Rappsilber, J.Allshire, R.C.Cook, A.G.Tuttelmann, F.O'Carroll, D.

(2024) Mol Cell 84: 1021

  • DOI: https://doi.org/10.1016/j.molcel.2024.01.014
  • Primary Citation of Related Structures:  
    8OU1

  • PubMed Abstract: 

    In the male mouse germ line, PIWI-interacting RNAs (piRNAs), bound by the PIWI protein MIWI2 (PIWIL4), guide DNA methylation of young active transposons through SPOCD1. However, the underlying mechanisms of SPOCD1-mediated piRNA-directed transposon methylation and whether this pathway functions to protect the human germ line remain unknown. We identified loss-of-function variants in human SPOCD1 that cause defective transposon silencing and male infertility. Through the analysis of these pathogenic alleles, we discovered that the uncharacterized protein C19ORF84 interacts with SPOCD1. DNMT3C, the DNA methyltransferase responsible for transposon methylation, associates with SPOCD1 and C19ORF84 in fetal gonocytes. Furthermore, C19ORF84 is essential for piRNA-directed DNA methylation and male mouse fertility. Finally, C19ORF84 mediates the in vivo association of SPOCD1 with the de novo methylation machinery. In summary, we have discovered a conserved role for the human piRNA pathway in transposon silencing and C19ORF84, an uncharacterized protein essential for orchestrating piRNA-directed DNA methylation.


  • Organizational Affiliation

    Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK. Electronic address: ansgar.zoch@ed.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPOC domain-containing protein 1
A, B
148Mus musculusMutation(s): 0 
Gene Names: Spocd1
UniProt
Find proteins for B1ASB6 (Mus musculus)
Explore B1ASB6 
Go to UniProtKB:  B1ASB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1ASB6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
C [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.52α = 90
b = 56.624β = 90
c = 97.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106144
Wellcome TrustUnited Kingdom200898
Wellcome TrustUnited Kingdom203149

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Database references