9Y61 | pdb_00009y61

Cryo-EM structure of ternary complex NSD2-PWWP1:CRBN:DDB1 in complex with NSD2-LDD, an LDD degrader

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone-lysine N-methyltransferase NSD2	protein-lysine N-methyltransferase activity histone H4 methyltransferase activity histone H4K20 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H4 methyltransferase activity histone H4K20 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3 methyltransferase activity chromatin binding binding histone H3K36 dimethyltransferase activity histone H3K36 methyltransferase activity sequence-specific DNA binding DNA binding nucleic acid binding histone H3K36 trimethyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	methylation metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process methylation metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nucleoplasm chromatin chromosome
B	Protein cereblon	protein binding binding transmembrane transporter binding cation binding ion binding metal ion binding small molecule binding	regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport localization regulation of transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport cellular process developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development animal gross anatomical part developmental process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of cellular component organization negative regulation of protein-containing complex assembly catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process behavior locomotory behavior exploration behavior locomotory exploration behavior	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006560	AWS domain	Domain
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR047441	Nuclear SET domain-containing protein 2, third PHD finger	Domain
A	IPR055197	Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger	Domain
A	IPR001214	SET domain	Domain
A	IPR000313	PWWP domain	Domain
A	IPR041306	NSD, Cys-His rich domain	Domain
A	IPR047426	Histone-lysine N-methyltransferase NSD1 / NSD2, first PHD finger	Domain
A	IPR050777	SET2 Histone-Lysine N-Methyltransferase	Family
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR047442	Nuclear SET domain-containing protein 2, fifth PHD finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR003616	Post-SET domain	Domain
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR055198	Histone-lysine N-methyltransferase NSD-like, PHD zinc finger	Domain
A	IPR047443	Nuclear SET domain-containing protein 2, HMG box	Domain
A	IPR047434	Nuclear SET domain-containing protein 2, first PWWP domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR047437	Nuclear SET domain-containing protein 2, SET domain	Domain
A	IPR047439	Nuclear SET domain-containing protein 2, second PHD finger	Domain
A	IPR047435	Nuclear SET domain-containing protein 2, second PWWP domain	Domain
A	IPR059153	Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1	Domain
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR009071	High mobility group box domain	Domain
A	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
B	IPR015947	PUA-like superfamily	Homologous Superfamily
B	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
B	IPR004910	Yippee/Mis18/Cereblon	Domain
B	IPR003111	Lon protease, N-terminal domain	Domain
B	IPR034750	CULT domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: O96028	Wolf-Hirschhorn syndrome breast carcinoma breast cancer Malignant neoplasm of breast medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma adrenal cortex carcinoma pituitary cancer bone marrow disease primitive neuroectodermal tumor cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma Wolf-Hirschhorn syndrome breast carcinoma breast cancer Malignant neoplasm of breast medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma adrenal cortex carcinoma pituitary cancer bone marrow disease primitive neuroectodermal tumor cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atopic eczema subependymal giant cell astrocytoma gastric carcinoma large cell medulloblastoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pilocytic astrocytoma atypical teratoid rhabdoid tumor childhood acute lymphoblastic leukemia glioblastoma malignant ependymoma
B	: Q96SW2	intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type lung adenocarcinoma myelodysplastic syndrome ovarian cancer

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.