7DE9 | pdb_00007de9

crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SNF	e7de9A1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: SNF	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth P]	Histone H3.2	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus
A	Transcriptional regulator	cohesin unloader activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity sequence-specific DNA binding DNA binding binding nucleic acid binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cell division cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cell division cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular component organization or biogenesis cell cycle cell cycle process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process homologous recombination DNA recombination developmental process multicellular organismal process sexual reproduction cellular developmental process reproductive process meiotic cell cycle developmental process involved in reproduction meiotic cell cycle process multicellular organism development gametophyte development microsporogenesis sexual sporulation anatomical structure development sporulation plant-type sporogenesis pollen development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome polymeric cytoskeletal fiber cytoskeleton supramolecular fiber microtubule supramolecular polymer supramolecular complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome polymeric cytoskeletal fiber cytoskeleton supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth P]	IPR000164	Histone H3/CENP-A	Family
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR039776	Sister chromatid cohesion protein Pds5	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P]	MLZ	Parent Component: LYS RESID: AA0076 PSI-MOD : N6-methyl-L-lysine MOD:00085
A	MSE	Parent Component: MET RESID: AA0076

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.