4X3E | pdb_00004x3e

Crystal structure of EED in complex with a trimethylated Jarid2 peptide

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cas_Cas5d	e4x3eA1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	ALA-GLN-ARG-M3L-PHE-ALA-GLN-SER	ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity chromatin binding binding protein binding ubiquitin binding ubiquitin-like protein binding DNA binding nucleic acid binding ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity chromatin binding binding protein binding ubiquitin binding ubiquitin-like protein binding DNA binding nucleic acid binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K27 methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development immune system development hematopoietic or lymphoid organ development thymus development immune system process central nervous system development developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development immune system development hematopoietic or lymphoid organ development thymus development immune system process central nervous system development nervous system development heart development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth tissue development striated muscle tissue development circulatory system development muscle cell proliferation cellular process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to pericentric heterochromatin protein localization to heterochromatin intracellular protein localization 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 metabolic process macromolecule metabolic process regulation of metabolic process regulation of growth regulation of cardiac muscle tissue growth regulation of developmental process negative regulation of biological process negative regulation of cardiac muscle tissue growth negative regulation of organ growth negative regulation of growth regulation of organ growth regulation of heart growth negative regulation of cellular process regulation of cardiac muscle cell proliferation regulation of multicellular organismal process negative regulation of cell population proliferation regulation of multicellular organismal development regulation of developmental growth negative regulation of heart growth negative regulation of developmental process negative regulation of developmental growth regulation of cell population proliferation negative regulation of multicellular organismal process negative regulation of cardiac muscle cell proliferation spleen development cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process facultative heterochromatin formation negative regulation of gene expression, epigenetic RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process stem cell differentiation cellular developmental process cell differentiation random inactivation of X chromosome sex-chromosome dosage compensation dosage compensation by inactivation of X chromosome response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm organelle lumen methyltransferase complex nuclear lumen PcG protein complex ESC/E(Z) complex membraneless organelle intracellular membraneless organelle chromatin chromosome
A	Polycomb protein EED	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding chromatin binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process multicellular organism development multicellular organismal process spinal cord development central nervous system development anatomical structure development nervous system development system development cellular developmental process neurogenesis gliogenesis oligodendrocyte differentiation glial cell differentiation cell differentiation cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression facultative heterochromatin formation negative regulation of gene expression, epigenetic sexual reproduction reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation epigenetic programming of gene expression multicellular organismal reproductive process genomic imprinting germ cell development transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II regulation of adaxial/abaxial pattern formation pattern specification process adaxial/abaxial pattern specification regionalization regulation of multicellular organismal process response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	intracellular anatomical structure sex chromosome intracellular membraneless organelle chromatin chromosome heterochromatin intracellular organelle sex chromatin cellular anatomical structure organelle membraneless organelle cytoplasm cytosol membrane-bounded organelle intracellular anatomical structure sex chromosome intracellular membraneless organelle chromatin chromosome heterochromatin intracellular organelle sex chromatin cellular anatomical structure organelle membraneless organelle cytoplasm cytosol membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex nucleoplasm organelle lumen methyltransferase complex ESC/E(Z) complex nuclear lumen chromatin silencing complex pronucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR003347	JmjC domain	Domain
B	IPR003349	JmjN domain	Domain
B	IPR001606	ARID DNA-binding domain	Domain
B	IPR004198	Zinc finger, C5HC2-type	Domain
B	IPR036431	ARID DNA-binding domain superfamily	Homologous Superfamily
A	IPR019775	WD40 repeat, conserved site	Conserved Site
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR001680	WD40 repeat	Repeat
A	IPR051243	Polycomb group WD repeat-containing protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q92833	autism spectrum disorder osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia tuberculosis Autism Spectrum Disorders ovarian cancer plasma cell myeloma squamous cell carcinoma lung cancer pancreatic intraductal papillary-mucinous carcinoma psoriasis subependymal giant cell astrocytoma
A	Pharos: O75530	schwannoma Cohen-Gibson syndrome malignant peripheral nerve sheath tumor perineurioma attention deficit hyperactivity disorder, inattentive type intellectual disability Nerve Sheath Tumors peripheral nervous system neoplasm Weaver syndrome epithelioid sarcoma cataract follicular lymphoma nerve sheath neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.