3OMG

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R14me2s

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8042395	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8042395	3000404	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SNase_1	e3omgA2	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SNase_1	ECOD (1.6)
A	TUDOR	e3omgA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)
B	SNase_1	e3omgB2	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SNase_1	ECOD (1.6)
B	TUDOR	e3omgB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00565	Staphylococcal nuclease homologue (SNase)	Staphylococcal nuclease homologue	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 1 ...	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Staphylococcal nuclease domain-containing protein 1	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA binding binding organic cyclic compound binding nucleic acid binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding cell adhesion molecule binding cadherin binding protein binding catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation regulation of biological process regulation of cellular process regulation of cell cycle process biological regulation cell cycle regulation of cell cycle cell cycle process developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation regulation of biological process regulation of cellular process regulation of cell cycle process biological regulation cell cycle regulation of cell cycle cell cycle process catabolic process RNA metabolic process primary metabolic process miRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process miRNA metabolic process macromolecule metabolic process RNA catabolic process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process mRNA catabolic process mRNA metabolic process	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol dense body protein-containing complex ribonucleoprotein complex RNAi effector complex nucleus
C, D	dimethylated arginine peptide R14me2s	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold	Domain
A, B	IPR002999	Tudor domain	Domain
A, B	IPR002071	Thermonuclease active site	Active Site
A, B	IPR047386	Tudor domain-containing protein 11, Tudor domain	Domain
A, B	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A, B	IPR016685	RNA-induced silencing complex, nuclease component Tudor-SN	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q7KZF4	astrocytic tumor Autistic Disorder myopathy attention deficit hyperactivity disorder, inattentive type large cell medulloblastoma pancreatic ductal adenocarcinoma autism lung benign neoplasm malignant pancreatic neoplasm psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	2MR	Parent Component: ARG RESID: AA0067 PSI-MOD : symmetric dimethyl-L-arginine MOD:00076

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.