9NFR | pdb_00009nfr

Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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	WD40 repeat-like	8052531	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Beta-Casp	e9nfrB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
A	Beta-Casp	e9nfrA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain
B	PF02190	ATP-dependent protease La (LON) substrate-binding domain (LON_substr_bdg)	ATP-dependent protease La (LON) substrate-binding domain	-	Family
B	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	PF10433	RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)	RSE1/DDB1/CPSF1 first beta-propeller	-	Repeat
A	PF23726	RSE1/DDB1/CPSF1 second beta-propeller (Beta-prop_RSE1_2nd)	RSE1/DDB1/CPSF1 second beta-propeller	-	Repeat
A	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Proto-oncogene vav	phosphoprotein binding phosphotyrosine residue binding protein binding binding protein phosphorylated amino acid binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding phosphoprotein binding phosphotyrosine residue binding protein binding binding protein phosphorylated amino acid binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding phosphorylation-dependent protein binding modification-dependent protein binding	cellular component organization regulation of cellular component size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus cellular component organization regulation of cellular component size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell migration cell motility lymphocyte mediated immunity biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process immune system process defense response to other organism response to stress natural killer cell mediated cytotoxicity innate immune response leukocyte mediated immunity response to external biotic stimulus natural killer cell mediated immunity cell killing multicellular organismal process regulation of body fluid levels wound healing cell activation hemostasis blood coagulation coagulation response to wounding platelet activation cell population proliferation B cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation natural killer cell activation immune response-regulating cell surface receptor signaling pathway cell surface receptor signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway Fc-epsilon receptor signaling pathway regulation of immune response regulation of immune system process small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway import into cell transport Fc-gamma receptor signaling pathway involved in phagocytosis vesicle-mediated transport localization immune response-activating signaling pathway positive regulation of immune response phagocytosis Fc-gamma receptor signaling pathway immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway establishment of localization endocytosis activation of immune response	cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane
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 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
A	DNA damage-binding protein 1	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding protein-containing complex binding protein binding cullin family protein binding damaged DNA binding WD40-repeat domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing catabolic process proteasomal protein catabolic process protein catabolic process protein metabolic process macromolecule catabolic process cell population proliferation regulation of biosynthetic process regulation of cellular process epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis regulation of metabolic process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process negative regulation of adipose tissue development connective tissue development adipose tissue development negative regulation of developmental process animal organ development negative regulation of biological process tissue development regulation of adipose tissue development anatomical structure development negative regulation of multicellular organismal process epigenetic programming of gene expression epigenetic programming in the zygotic pronuclei regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle mitotic cell cycle phase transition cell cycle process DNA repair positive regulation of viral genome replication positive regulation of viral process positive regulation of biological process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of macromolecule metabolic process negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression regulation of post-transcriptional gene silencing negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV monosaccharide metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process rhythmic process circadian rhythm regulation of circadian rhythm positive regulation of protein metabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process regulation of cellular response to stress regulation of response to stimulus regulation of response to stress biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell regulation of biological quality proteasome-mediated ubiquitin-dependent protein catabolic process regulation of DNA-templated DNA replication initiation DNA replication initiation regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process exit from host cell viral release from host cell biological process involved in interaction with host regulation of cell population proliferation meiotic chromosome segregation microtubule cytoskeleton organization membraneless organelle assembly female gamete generation meiotic cell cycle process cellular component biogenesis cellular component assembly female meiotic nuclear division meiotic nuclear division chromosome segregation spindle organization organelle assembly organelle fission meiotic cell cycle meiotic spindle organization meiotic spindle assembly spindle assembly nuclear division organelle organization nuclear chromosome segregation microtubule-based process cytoskeleton organization spindle assembly involved in female meiosis regulation of embryonic development regulation of multicellular organismal development embryo development multicellular organism development autophagy regulation of autophagy process utilizing autophagic mechanism regulation of cytokinesis cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis regulation of cell division regulation of mitotic cytokinesis cell division regulation of leukocyte activation cell activation regulation of cell activation natural killer cell activation lymphocyte activation leukocyte activation immune system process regulation of immune system process regulation of natural killer cell activation regulation of lymphocyte activation	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle intracellular membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen 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 nucleoplasm site of double-strand break site of DNA damage Cul4B-RING E3 ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR003096	Smooth muscle protein/calponin	Family
C	IPR001849	Pleckstrin homology domain	Domain
C	IPR036860	SH2 domain superfamily	Homologous Superfamily
C	IPR000980	SH2 domain	Domain
C	IPR000219	Dbl homology domain	Domain
C	IPR001715	Calponin homology domain	Domain
C	IPR036028	SH3-like domain superfamily	Homologous Superfamily
C	IPR035730	VAV1 protein, first SH3 domain	Domain
C	IPR011993	PH-like domain superfamily	Homologous Superfamily
C	IPR001331	Guanine-nucleotide dissociation stimulator, CDC24, conserved site	Conserved Site
C	IPR035729	VAV1 protein, second SH3 domain	Domain
C	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
C	IPR022613	CASAMP, second calponin-homology domain	Domain
C	IPR001452	SH3 domain	Domain
C	IPR035879	VAV1, SH2 domain	Domain
C	IPR036872	CH domain superfamily	Homologous Superfamily
C	IPR037832	Vav, PH domain	Domain
C	IPR035899	Dbl homology (DH) 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
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR058543	RSE1/DDB1/CPSF1, second beta-propeller	Domain
A	IPR004871	RSE1/DDB1/CPSF1, C-terminal	Domain
A	IPR050358	RSE1/DDB1/CPSF1	Family
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR018846	RSE1/DDB1/CPSF1, first beta-propeller	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	: P15498	adult T-cell leukemia/lymphoma medulloblastoma childhood medulloblastoma Liver Cirrhosis, Experimental medullomyoblastoma with myogenic differentiation adult medulloblastoma melanotic medulloblastoma acute T cell leukemia interstitial cystitis osteosarcoma wet macular degeneration age-related macular degeneration cutaneous lupus erythematosus spina bifida cancer adult T-cell leukemia/lymphoma medulloblastoma childhood medulloblastoma Liver Cirrhosis, Experimental medullomyoblastoma with myogenic differentiation adult medulloblastoma melanotic medulloblastoma acute T cell leukemia interstitial cystitis osteosarcoma wet macular degeneration age-related macular degeneration cutaneous lupus erythematosus spina bifida cancer desmoplastic/nodular medulloblastoma lung adenocarcinoma subependymal giant cell astrocytoma
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
A	: Q16531	Disease Exacerbation gastric cancer lung cancer xeroderma pigmentosum gastric neoplasm drug-induced liver injury hereditary diffuse gastric adenocarcinoma psoriasis

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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.