8OU1 | pdb_00008ou1

Crystal structure of the SPOC domain of mouse SPOCD1

PDB DOI: https://doi.org/10.2210/pdb8OU1/pdb

Classification: GENE REGULATION
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-21 Released: 2024-02-21
Deposition Author(s): Heep, M., Cook, A.G., O'Carroll, D.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (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

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

PubMed: 38359823 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.molcel.2024.01.014
Primary Citation 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.

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.

Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.

Institute of Reproductive Genetics, University of Münster, Münster, Germany.

Institute for Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford OX37TY, UK.

Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany.

School of BioSciences and Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia.

Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA.

Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA.

Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA.

Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.

Macromolecule Content

Total Structure Weight: 32.91 kDa
Atom Count: 2,482
Modeled Residue Count: 287
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPOC domain-containing protein 1	A, B	148	Mus musculus	Mutation(s): 0 Gene Names: Spocd1
UniProt
Find proteins for B1ASB6 (Mus musculus) Explore B1ASB6 Go to UniProtKB: B1ASB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1ASB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]