9Q03 | pdb_00009q03

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)

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)
A	SCOP2B Superfamily	POZ domain	8040250	3000894	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	POZ domain	8040250	3000894	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF02190	ATP-dependent protease La (LON) substrate-binding domain (LON_substr_bdg)	ATP-dependent protease La (LON) substrate-binding domain	-	Family
C	PF03226	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly (Yippee-Mis18)	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of ...	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus [5]. This entry also includes the CULT domain proteins such as Cereblon [6].	Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	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 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 proteolysis involved in protein 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 proteolysis ubiquitin-dependent protein catabolic process behavior multicellular organismal process 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
A, B	B-cell lymphoma 6 protein	sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding double-stranded DNA binding identical protein binding protein binding transcription factor binding transcription coregulator binding transcription corepressor binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding double-stranded DNA binding identical protein binding protein binding transcription factor binding transcription coregulator binding transcription corepressor binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding intronic transcription regulatory region sequence-specific DNA binding chromatin DNA binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of leukocyte proliferation regulation of biological process negative regulation of cell population proliferation cell population proliferation regulation of cellular process biological regulation negative regulation of biological process leukocyte proliferation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of cell population proliferation mononuclear cell proliferation negative regulation of cellular process regulation of mononuclear cell proliferation localization macromolecule localization intracellular protein localization multicellular organismal process regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte activation T cell activation lymphocyte proliferation regulation of immune system process regulation of multicellular organismal process T cell proliferation regulation of lymphocyte proliferation cell activation regulation of T cell activation regulation of T cell proliferation immune system process regulation of lymphocyte activation erythrocyte development cellular developmental process homeostatic process hemopoiesis cell development erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation cell differentiation anatomical structure development myeloid cell development homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis immunological memory formation process regulation of immune effector process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response regulation of cell development multicellular organism development T cell differentiation immune response immune effector process regulation of response to stimulus regulation of immune response leukocyte differentiation regulation of developmental process regulation of T cell differentiation memory T cell differentiation T cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development T cell differentiation involved in immune response regulation of memory T cell differentiation regulation of hemopoiesis immunological memory process negative regulation of mast cell cytokine production cytokine production regulation of cytokine production mast cell cytokine production myeloid leukocyte cytokine production cytokine production involved in immune response negative regulation of macromolecule metabolic process production of molecular mediator of immune response regulation of biosynthetic process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of mast cell cytokine production negative regulation of metabolic process negative regulation of immune effector process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of production of molecular mediator of immune response negative regulation of gene expression biosynthetic process negative regulation of immune system process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response negative regulation of multicellular organismal process regulation of metabolic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process regulation of alpha-beta T cell activation alpha-beta T cell differentiation involved in immune response negative regulation of cell adhesion negative regulation of T cell differentiation type 2 immune response regulation of T-helper cell differentiation regulation of type 2 immune response alpha-beta T cell activation T-helper cell differentiation negative regulation of leukocyte differentiation negative regulation of type 2 immune response negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion CD4-positive, alpha-beta T cell differentiation negative regulation of T-helper 2 cell differentiation alpha-beta T cell differentiation regulation of T-helper 2 cell differentiation negative regulation of cell differentiation regulation of cell-cell adhesion negative regulation of developmental process regulation of cell adhesion negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of alpha-beta T cell activation CD4-positive, alpha-beta T cell differentiation involved in immune response negative regulation of hemopoiesis negative regulation of immune response negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of lymphocyte differentiation negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation leukocyte cell-cell adhesion cell adhesion cell-cell adhesion alpha-beta T cell activation involved in immune response CD4-positive, alpha-beta T cell activation T-helper 2 cell differentiation negative regulation of response to stimulus negative regulation of T-helper cell differentiation negative regulation of cell activation regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization anatomical structure morphogenesis cell morphogenesis positive regulation of cell population proliferation positive regulation of B cell proliferation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation positive regulation of immune system process B cell activation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility cell motility locomotion mature B cell differentiation B cell activation involved in immune response regulation of plasma cell differentiation plasma cell differentiation negative regulation of plasma cell differentiation regulation of B cell differentiation B cell differentiation negative regulation of B cell activation negative regulation of B cell differentiation mature B cell differentiation involved in immune response 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 small GTPase-mediated signal transduction signaling Rho protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains system development negative regulation of immunoglobulin production negative regulation of B cell mediated immunity DNA recombination DNA metabolic process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of immunoglobulin mediated immune response B cell mediated immunity regulation of DNA metabolic process immunoglobulin production somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments regulation of immunoglobulin mediated immune response regulation of isotype switching somatic diversification of immune receptors via germline recombination within a single locus negative regulation of DNA metabolic process negative regulation of leukocyte mediated immunity lymphocyte mediated immunity regulation of DNA recombination negative regulation of lymphocyte mediated immunity regulation of isotype switching to IgE isotypes negative regulation of isotype switching to IgE isotypes leukocyte mediated immunity somatic diversification of immune receptors somatic recombination of immunoglobulin genes involved in immune response regulation of adaptive immune response negative regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins negative regulation of DNA recombination regulation of leukocyte mediated immunity negative regulation of isotype switching isotype switching immune system development immunoglobulin production involved in immunoglobulin-mediated immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains isotype switching to IgE isotypes adaptive immune response immunoglobulin mediated immune response regulation of immunoglobulin production regulation of lymphocyte mediated immunity mitotic DNA replication negative regulation of nuclear cell cycle DNA replication nuclear DNA replication negative regulation of cell cycle cell cycle DNA replication mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of DNA-templated DNA replication cell cycle regulation of cell cycle cell cycle process DNA-templated DNA replication negative regulation of DNA replication regulation of mitotic cell cycle DNA replication regulation of nuclear cell cycle DNA replication regulation of cell cycle process negative regulation of cell cycle process DNA replication mitotic cell cycle process regulation of DNA-templated DNA replication negative regulation of mitotic cell cycle DNA replication regulation of DNA replication regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of B cell apoptotic process negative regulation of programmed cell death leukocyte apoptotic process B cell apoptotic process negative regulation of B cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of lymphocyte apoptotic process cell-matrix adhesion cell-substrate adhesion positive regulation of T cell differentiation positive regulation of developmental process positive regulation of T cell activation positive regulation of cell development positive regulation of regulatory T cell differentiation positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation positive regulation of cell adhesion regulation of regulatory T cell differentiation regulatory T cell differentiation positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of germinal center formation anatomical structure formation involved in morphogenesis germinal center formation regulation of anatomical structure morphogenesis negative regulation of signaling regulation of signal transduction negative regulation of cell communication regulation of signaling cell surface receptor signaling pathway negative regulation of signal transduction Notch signaling pathway negative regulation of Notch signaling pathway regulation of Notch signaling pathway regulation of cell communication negative regulation of Rho protein signal transduction regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction regulation of intracellular signal transduction negative regulation of small GTPase mediated signal transduction regulation of Rho protein signal transduction positive regulation of neuron differentiation neurogenesis neuron differentiation nervous system development generation of neurons regulation of neuron differentiation regulation of defense response regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus regulation of response to stress inflammatory response regulation of cellular senescence cellular senescence negative regulation of cellular senescence cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression, epigenetic regulation of cell-substrate adhesion negative regulation of cell-matrix adhesion regulation of cell-matrix adhesion negative regulation of cell-substrate adhesion central nervous system neuron differentiation central nervous system development pyramidal neuron differentiation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex paraspeckles nuclear ribonucleoprotein granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR015947	PUA-like superfamily	Homologous Superfamily
C	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
C	IPR004910	Yippee/Mis18/Cereblon	Domain
C	IPR003111	Lon protease, N-terminal domain	Domain
C	IPR034750	CULT domain	Domain
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, B	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, B	IPR000210	BTB/POZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: 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
A, B	Pharos: P41182	follicular lymphoma T-cell non-Hodgkin lymphoma lung carcinoma Lymphoma, Intermediate-Grade malignant mesothelioma adenoma medulloblastoma atypical teratoid rhabdoid tumor osteosarcoma cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary mediastinal large B-cell lymphoma gastric carcinoma hydrolethalus syndrome spondyloarthropathy follicular lymphoma T-cell non-Hodgkin lymphoma lung carcinoma Lymphoma, Intermediate-Grade malignant mesothelioma adenoma medulloblastoma atypical teratoid rhabdoid tumor osteosarcoma cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary mediastinal large B-cell lymphoma gastric carcinoma hydrolethalus syndrome spondyloarthropathy ulcerative colitis lymphoma lymphosarcoma malignant pancreatic neoplasm non-Hodgkin lymphoma B-cell chronic lymphocytic leukemia ovarian cancer Crohn disease Pick disease ductal breast carcinoma in situ primitive neuroectodermal tumor glioblastoma reticulum cell sarcoma invasive ductal breast carcinoma subependymal giant cell astrocytoma lung cancer malignant ependymoma MALT lymphoma astrocytic tumor oligodendroglioma breast carcinoma pancreatic ductal adenocarcinoma dermatomyositis pituitary cancer psoriasis rheumatoid arthritis large cell medulloblastoma

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.