Annotations: 6OIT

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Hypothetical protein At3g22680	8041365	3001432	SCOP2B (2022-06-29)
B	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)
A	RdDM_RDM1	e6oitA1	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)
B	RdDM_RDM1	e6oitB1	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)
C	SMC_hinge	e6oitC1	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)
D	SMC_hinge	e6oitD1	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	e6oitE1	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	e6oitF1	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)

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 (utative)
B	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
A, B	Protein RDM1	DNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing 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 metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular component organization siRNA-mediated heterochromatin formation chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated 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 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
C, D, E, F	Protein DEFECTIVE IN MERISTEM SILENCING 3	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	regulation of cellular 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 regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of cellular 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 regulation of biological process 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 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 metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular component organization siRNA-mediated heterochromatin formation chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated 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 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
G	Protein CHROMATIN REMODELING 35	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity hydrolase activity ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA	cellular component organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress cellular component organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to fungus defense response to other organism response to stress response to external biotic stimulus response to fungus regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process siRNA-mediated heterochromatin formation negative regulation of cellular process DNA methylation-dependent heterochromatin formation chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation 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 constitutive heterochromatin formation 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 gene silencing by siRNA-directed DNA methylation macromolecule metabolic process regulation of metabolic process cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA cellular response to exogenous dsRNA cellular response to organic cyclic compound response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical response to organic cyclic compound negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization regulation of DNA methylation-dependent heterochromatin formation regulation of cellular component organization positive regulation of biological process positive regulation of cellular metabolic process negative regulation of chromatin organization positive regulation of biosynthetic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process positive regulation of chromatin binding regulation of molecular function positive regulation of molecular function regulation of binding regulation of chromatin binding positive regulation of binding	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 transcription regulator complex RNA polymerase IV transcription regulator complex pericentric heterochromatin chromatin chromosome heterochromatin chromosomal region intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle

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
G	IPR000330	SNF2, N-terminal	Domain
G	IPR001650	Helicase, C-terminal domain-like	Domain
G	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
G	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
G	IPR044567	SNF2 domain-containing protein CLSY/DRD1	Family
G	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.