Annotations: 6OIS

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Hypothetical protein At3g22680	8041365	3001432	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hypothetical protein At3g22680	8041365	3001432	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)
D	SMC_hinge	e6oisD1	A: a+b duplicates or obligate multimers	X: Smc hinge domain (From Topology)	H: Smc hinge domain (From Topology)	T: Smc hinge domain	F: SMC_hinge	ECOD (1.6)
F	SMC_hinge	e6oisF1	A: a+b duplicates or obligate multimers	X: Smc hinge domain (From Topology)	H: Smc hinge domain (From Topology)	T: Smc hinge domain	F: SMC_hinge	ECOD (1.6)
E	SMC_hinge	e6oisE1	A: a+b duplicates or obligate multimers	X: Smc hinge domain (From Topology)	H: Smc hinge domain (From Topology)	T: Smc hinge domain	F: SMC_hinge	ECOD (1.6)
C	SMC_hinge	e6oisC1	A: a+b duplicates or obligate multimers	X: Smc hinge domain (From Topology)	H: Smc hinge domain (From Topology)	T: Smc hinge domain	F: SMC_hinge	ECOD (1.6)
B	RdDM_RDM1	e6oisB1	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)
A	RdDM_RDM1	e6oisA1	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)
B	1.20.120.690	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	RDM1 protein domain	CATH (utative)
A	1.20.120.690	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	RDM1 protein domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
C, D, E, F	Protein DEFECTIVE IN MERISTEM SILENCING 3	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process cellular component organization cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic gene silencing by siRNA-directed DNA methylation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
A, B	Protein RDM1	DNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing 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 metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular component organization cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic gene silencing by siRNA-directed DNA methylation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure 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, B	IPR015270	Protein RDM1, plant	Family
A, B	IPR036319	RDM1 superfamily	Homologous Superfamily

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.