8VOJ

The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8088480	3000260	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07707	BTB And C-terminal Kelch (BACK)	BTB And C-terminal Kelch	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD ...	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, personal observation).	Domain
A, B	PF07646	Kelch motif (Kelch_2)	Kelch motif	-	Repeat
A, B	PF00651	BTB/POZ domain (BTB)	BTB/POZ domain	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family o ...	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.	Domain
C	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain
D	PF01448	ELM2 domain (ELM2)	ELM2 domain	-	Family
D	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Isoform 2 of Kelch repeat and BTB domain-containing protein 4	-	-	-
C	Histone deacetylase 1	Krueppel-associated box domain binding protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding Krueppel-associated box domain binding protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity chromatin binding promoter-specific chromatin binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding histone deacetylase activity p53 binding transcription coregulator binding transcription corepressor binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity protein decrotonylase activity histone decrotonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds E-box binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication rhythmic process circadian regulation of gene expression circadian rhythm positive regulation of signaling receptor activity regulation of signaling receptor activity positive regulation of molecular function regulation of molecular function negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway protein deacylation macromolecule modification primary metabolic process protein metabolic process macromolecule deacylation protein modification process protein deacetylation negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation epithelium development epidermal cell differentiation epidermis development anatomical structure development tissue development epithelial cell differentiation multicellular organismal process negative regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance negative regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number negative regulation of multicellular organismal 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 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 negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular component organization chromatin organization cellular component organization or biogenesis ectodermal placode morphogenesis molting cycle process hair cycle animal organ development hair follicle placode formation ectodermal placode formation anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle anatomical structure formation involved in morphogenesis ectodermal placode development hair cycle process head development forebrain development brain development nervous system development pallium development multicellular organism development central nervous system development telencephalon development hippocampus development limbic system development system development viral gene expression biological process involved in interspecies interaction between organisms negative regulation by host of viral transcription modulation by host of symbiont process viral process biological process involved in interaction with symbiont viral transcription biological process involved in symbiotic interaction neurogenesis gliogenesis oligodendrocyte differentiation glial cell differentiation cellular response to platelet-derived growth factor stimulus response to platelet-derived growth factor regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process endoderm development generation of neurons neuron differentiation regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic heterochromatin formation constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation positive regulation of nervous system development cell development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of multicellular organismal development regulation of glial cell differentiation positive regulation of cell development positive regulation of glial cell differentiation regulation of oligodendrocyte differentiation eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway negative regulation of intracellular steroid hormone receptor signaling pathway response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus cellular response to organic cyclic compound regulation of androgen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid negative regulation of androgen receptor signaling pathway nuclear receptor-mediated signaling pathway tongue development fungiform papilla formation fungiform papilla development sensory organ morphogenesis fungiform papilla morphogenesis tongue morphogenesis limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development appendage morphogenesis embryonic digit morphogenesis limb morphogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex ATPase complex nucleus cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle protein-containing complex ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular organelle lumen histone deacetylase complex nucleoplasm NuRD complex SWI/SNF superfamily-type complex catalytic complex intracellular membrane-bounded organelle organelle lumen CHD-type complex nuclear lumen heterochromatin somatodendritic compartment cell body neuronal cell body Sin3-type complex nuclear chromosome transcription repressor complex
D	REST corepressor 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding protein binding enzyme 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 multicellular organismal process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation positive regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process positive regulation of megakaryocyte differentiation positive regulation of cellular process developmental process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostatic process erythrocyte differentiation multicellular organismal-level homeostasis homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of gene expression cellular component organization chromatin organization cellular component organization or biogenesis	protein-containing complex catalytic complex DNA repair complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure protein-containing complex catalytic complex DNA repair complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015915	Kelch-type beta propeller	Homologous Superfamily
A, B	IPR042884	Kelch repeat and BTB domain-containing protein 4	Family
A, B	IPR011498	Kelch repeat type 2	Repeat
A, B	IPR042949	KBTBD4, BTB/POZ domain	Domain
A, B	IPR017096	BTB-kelch protein	Family
A, B	IPR011705	BTB/Kelch-associated	Domain
A, B	IPR000210	BTB/POZ domain	Domain
A, B	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, B	IPR042950	KBTBD4, BACK domain	Domain
C	IPR000286	Histone deacetylase family	Family
C	IPR023801	Histone deacetylase domain	Domain
C	IPR003084	Histone deacetylase	Family
C	IPR050284	Histone deacetylase and polyamine deacetylase	Family
C	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
C	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
D	IPR051066	Transcriptional Regulator and Corepressor	Family
D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D	IPR049048	REST corepressor, helical domain	Domain
D	IPR017884	SANT domain	Domain
D	IPR001005	SANT/Myb domain	Domain
D	IPR000949	ELM2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9NVX7	endogenous depression malignant ependymoma osteosarcoma hypertensive disorder medulloblastoma ovarian cancer lung cancer metabolic syndrome X subependymal giant cell astrocytoma
C	Pharos: Q13547	squamous cell carcinoma plasma cell myeloma endometriosis heart disease Familial Primary Pulmonary Hypertension osteosarcoma pancreatic intraductal papillary-mucinous neoplasm acute T cell leukemia schizophrenia atypical teratoid rhabdoid tumor glioblastoma idiopathic pulmonary arterial hypertension malignant ependymoma medulloblastoma ovarian cancer squamous cell carcinoma plasma cell myeloma endometriosis heart disease Familial Primary Pulmonary Hypertension osteosarcoma pancreatic intraductal papillary-mucinous neoplasm acute T cell leukemia schizophrenia atypical teratoid rhabdoid tumor glioblastoma idiopathic pulmonary arterial hypertension malignant ependymoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary cutaneous T-cell lymphoma adult T-cell leukemia/lymphoma breast cancer lung cancer malignant glioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor astrocytic tumor subependymal giant cell astrocytoma cancer hematologic disease lymphoplasmacytic lymphoma mature T-cell and NK-cell non-Hodgkin lymphoma
D	Pharos: Q9UKL0	malignant colon neoplasm allergic rhinitis dermatomyositis ovarian cancer benign colon neoplasm IgA glomerulonephritis malignant glioma colonic neoplasm large cell medulloblastoma medulloblastoma