1VK5

X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vk5a_	All alpha proteins	Hypothetical protein At3g22680	Hypothetical protein At3g22680	Hypothetical protein At3g22680	Hypothetical protein At3g22680	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Hypothetical protein At3g22680	8028986	4002573	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Hypothetical protein At3g22680	8041365	3001432	SCOP2 (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	RdDM_RDM1	e1vk5A1	A: alpha arrays	X: Hypothetical protein At3g22680 (From Topology)	H: Hypothetical protein At3g22680 (From Topology)	T: Hypothetical protein At3g22680	F: RdDM_RDM1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.690	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	RDM1 protein domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09187	RNA-directed DNA methylation 1 (RdDM_RDM1)	RNA-directed DNA methylation 1	This family of plant proteins includes RDM1 from Arabidopsis, which is a component of the RNA-directed DNA methylation (RdDM) effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation [1]. As ...	This family of plant proteins includes RDM1 from Arabidopsis, which is a component of the RNA-directed DNA methylation (RdDM) effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation [1]. As part of the DDR complex with two other RdDM components, it has been shown to facilitate association of PolV to chromatin [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	expressed protein	DNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression regulatory ncRNA-mediated heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process facultative heterochromatin formation gene silencing by siRNA-directed DNA methylation macromolecule metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA processing primary metabolic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing organic cyclic compound metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015270	Protein RDM1, plant	Family
A	IPR036319	RDM1 superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.