2OO4 | pdb_00002oo4

Structure of LNR-HD (Negative Regulatory Region) from human Notch 2

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	NOD	e2oo4A4	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
A	Notch	e2oo4A1	A: few secondary structure elements	X: Lin12/Notch repeat (From Topology)	H: Lin12/Notch repeat (From Topology)	T: Lin12/Notch repeat	F: Notch	ECOD (1.6)
B	NOD	e2oo4B1	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
B	Notch	e2oo4B2	A: few secondary structure elements	X: Lin12/Notch repeat (From Topology)	H: Lin12/Notch repeat (From Topology)	T: Lin12/Notch repeat	F: Notch	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.300.320	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.30.70.3310	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.300.320	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.30.70.3310	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06816	NOTCH protein (NOD)	NOTCH protein	-	Family
A, B	PF07684	NOTCH protein (NODP)	NOTCH protein	-	Family
A, B	PF00066	LNR domain (Notch)	LNR domain	The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR [1] and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats ar ...	The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR [1] and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Neurogenic locus notch homolog protein 2	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding NF-kappaB binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding NF-kappaB binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding ion binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity enzyme binding	cholangiocyte proliferation cell population proliferation cellular process epithelial cell proliferation developmental process tissue morphogenesis anatomical structure morphogenesis epithelium development anatomical structure development morphogenesis of an epithelium tissue development morphogenesis of an epithelial sheet multicellular organismal process myeloid leukocyte differentiation cholangiocyte proliferation cell population proliferation cellular process epithelial cell proliferation developmental process tissue morphogenesis anatomical structure morphogenesis epithelium development anatomical structure development morphogenesis of an epithelium tissue development morphogenesis of an epithelial sheet multicellular organismal process myeloid leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process cell development regulation of cell differentiation regulation of cell development multicellular organism development skeletal system development cell differentiation bone cell development osteoclast differentiation regulation of immune system process regulation of multicellular organismal process regulation of osteoclast development bone development system development regulation of biological process regulation of multicellular organismal development hemopoiesis animal organ development biological regulation osteoclast development myeloid cell differentiation immune system process myeloid cell development regulation of hemopoiesis leukocyte differentiation apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process camera-type eye morphogenesis sensory organ development ciliary body morphogenesis eye development visual system development eye morphogenesis sensory organ morphogenesis camera-type eye development animal organ morphogenesis sensory system development defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus placenta blood vessel development placenta development vasculature development circulatory system development blood vessel development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of miRNA transcription embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development immune response inflammatory response inflammatory response to antigenic stimulus mononuclear cell differentiation mature B cell differentiation B cell activation involved in immune response lymphocyte activation cell activation involved in immune response lymphocyte differentiation marginal zone B cell differentiation leukocyte activation B cell differentiation leukocyte activation involved in immune response lymphocyte activation involved in immune response mature B cell differentiation involved in immune response B cell activation cell activation immune effector process nervous system development glomerulus vasculature morphogenesis angiogenesis renal system development kidney vasculature development renal system vasculature development tube morphogenesis glomerular capillary formation nephron development blood vessel morphogenesis tube development glomerulus development glomerulus morphogenesis anatomical structure formation involved in morphogenesis glomerulus vasculature development kidney development kidney vasculature morphogenesis renal system vasculature morphogenesis negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process kidney epithelium development proximal tubule development nephron tubule development renal tubule development nephron epithelium development multicellular organism growth developmental growth growth smooth muscle cell differentiation positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cellular response to stimulus cell surface receptor signaling pathway signaling cell communication Notch signaling pathway signal transduction cellular response to biotic stimulus response to tumor cell cellular response to tumor cell positive regulation of transcription by RNA polymerase II heart morphogenesis pattern specification process embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry epithelial tube morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis heart development embryonic morphogenesis determination of heart left/right asymmetry regionalization left/right pattern formation tissue remodeling bone remodeling cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cell population proliferation positive regulation of keratinocyte proliferation positive regulation of epithelial cell proliferation regulation of keratinocyte proliferation regulation of cell population proliferation regulation of epithelial cell proliferation keratinocyte proliferation cardiac atrium morphogenesis cardiac chamber morphogenesis cardiac atrium development cardiac septum development cardiac septum morphogenesis cardiac chamber development atrial septum morphogenesis atrial septum development myeloid dendritic cell activation myeloid leukocyte activation myeloid dendritic cell differentiation dendritic cell differentiation positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling humoral immune response gland development liver development common bile duct development hepaticobiliary system development intrahepatic bile duct development negative regulation of programmed cell death negative regulation of apoptotic process renal filtration cell differentiation glomerular epithelial cell differentiation epithelial cell differentiation epithelial cell differentiation involved in kidney development glomerular epithelium development podocyte development epithelial cell development cell differentiation involved in kidney development glomerular epithelial cell development podocyte differentiation limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis left/right axis specification axis specification epithelial cell proliferation involved in liver morphogenesis gland morphogenesis hepatocyte proliferation liver morphogenesis regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of BMP signaling pathway regulation of BMP signaling pathway regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cell fate determination cell fate commitment pulmonary valve morphogenesis heart valve development pulmonary valve development heart valve morphogenesis semi-lunar valve development wound healing response to wounding cardiac conduction system development cardiac muscle tissue development striated muscle tissue development atrioventricular node development muscle tissue development negative regulation of gene expression small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of Ras protein signal transduction positive regulation of Ras protein signal transduction Ras protein signal transduction positive regulation of small GTPase mediated signal transduction regulation of leukocyte differentiation positive regulation of osteoclast differentiation regulation of osteoclast differentiation positive regulation of hemopoiesis positive regulation of immune system process regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of myeloid cell differentiation positive regulation of multicellular organismal process positive regulation of leukocyte differentiation	cellular anatomical structure membrane protein-containing complex receptor complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system Golgi membrane bounding membrane of organelle cellular anatomical structure membrane protein-containing complex receptor complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system Golgi membrane bounding membrane of organelle organelle membrane cell projection cilium plasma membrane bounded cell projection cell surface cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR010660	Notch, NOD domain	Domain
A, B	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A, B	IPR013032	EGF-like, conserved site	Conserved Site
A, B	IPR002110	Ankyrin repeat	Repeat
A, B	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
A, B	IPR001881	EGF-like calcium-binding domain	Domain
A, B	IPR008297	Notch	Family
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR000800	Notch domain	Domain
A, B	IPR024600	Notch, C-terminal	Domain
A, B	IPR000742	EGF-like domain	Domain
A, B	IPR051355	Notch and Slit guidance protein	Family
A, B	IPR035993	Notch-like domain superfamily	Homologous Superfamily
A, B	IPR022336	Neurogenic locus notch homolog protein 2	Family
A, B	IPR011656	Notch, NODP domain	Domain
A, B	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A, B	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q04721	acroosteolysis dominant type glioblastoma Alagille syndrome astrocytic tumor Alagille syndrome due to a NOTCH2 point mutation pilocytic astrocytoma esophageal squamous cell carcinoma medulloblastoma giant cell glioblastoma subependymal giant cell astrocytoma childhood cerebral astrocytoma medulloepithelioma ependymoblastoma fibrillary astrocytoma skin cancer acroosteolysis dominant type glioblastoma Alagille syndrome astrocytic tumor Alagille syndrome due to a NOTCH2 point mutation pilocytic astrocytoma esophageal squamous cell carcinoma medulloblastoma giant cell glioblastoma subependymal giant cell astrocytoma childhood cerebral astrocytoma medulloepithelioma ependymoblastoma fibrillary astrocytoma skin cancer breast carcinoma cerebral primitive neuroectodermal tumor gemistocytic astrocytoma anaplastic astrocytoma protoplasmic astrocytoma juvenile pilocytic astrocytoma skin neoplasm squamous cell carcinoma type 2 diabetes mellitus cervical cancer urinary bladder neoplasm Cholestasis in newborn malignant mesothelioma digestive system neuroendocrine neoplasm Emery-Dreifuss muscular dystrophy myopathy Alagille syndrome due to a JAG1 point mutation ovarian cancer bladder benign neoplasm psoriasis breast cancer large cell medulloblastoma cerebral astrocytoma lung carcinoma urinary bladder cancer malignant ependymoma chronic obstructive pulmonary disease diffuse astrocytoma Down syndrome acute myeloid leukemia osteogenesis imperfecta astrocytoma (excluding glioblastoma) hydrocephalus primitive neuroectodermal tumor bladder carcinoma in situ juvenile dermatomyositis lung benign neoplasm transitional cell carcinoma urinary bladder carcinoma cholestasis malignant glioma Crohn disease diffuse large B-cell lymphoma maturity-onset diabetes of the young Duchenne muscular dystrophy osteosarcoma pituitary cancer atypical teratoid rhabdoid tumor intellectual disability breast adenocarcinoma cancer lung cancer lymphoma

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.