Annotations: 2OO4

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)
B	HTHP	e2oo4B1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.2)
A	NOD,NODP	e2oo4A1	A: beta barrels	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: NOD,NODP	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06816	NOTCH protein (NOD)	NOTCH protein	NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals [1-2]. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3 ...	NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals [1-2]. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.	Domain
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 cation binding ion binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity transcription coactivator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding NF-kappaB binding cation binding ion binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity enzyme binding	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 anatomical structure development 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 anatomical structure development regulation of immune system process regulation of multicellular organismal process regulation of osteoclast development bone development system development developmental process 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 cellular process leukocyte differentiation apoptotic process cell death programmed cell death RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic 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 positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of miRNA transcription response to 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 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 development blood vessel morphogenesis tube development vasculature development circulatory system development glomerulus development anatomical structure morphogenesis glomerulus morphogenesis anatomical structure formation involved in morphogenesis glomerulus vasculature development kidney development kidney vasculature morphogenesis renal system vasculature morphogenesis epithelium development kidney epithelium development proximal tubule development nephron tubule development tissue development renal tubule development nephron epithelium development 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 response to biotic stimulus cellular response to tumor cell transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II heart morphogenesis pattern specification process embryo development embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry animal organ morphogenesis epithelial tube morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis heart development embryonic morphogenesis morphogenesis of an epithelium determination of heart left/right asymmetry regionalization tissue morphogenesis left/right pattern formation tissue remodeling bone remodeling cell population proliferation 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 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 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 negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular 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 left/right axis specification axis specification cell fate determination cell fate commitment pulmonary valve morphogenesis heart valve development pulmonary valve development heart valve morphogenesis semi-lunar valve development axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development wound healing response to stress response to wounding cardiac conduction system development cardiac muscle tissue development striated muscle tissue development atrioventricular node development muscle tissue development negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process 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 signaling receptor complex membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm cellular anatomical structure membrane protein-containing complex signaling receptor complex membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm 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	IPR001881	EGF-like calcium-binding domain	Domain
A, B	IPR008297	Notch	Family
A, B	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
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	: Q04721	acroosteolysis dominant type glioblastoma Alagille syndrome astrocytic tumor pilocytic astrocytoma Alagille syndrome due to a NOTCH2 point mutation 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 pilocytic astrocytoma Alagille syndrome due to a NOTCH2 point mutation 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 skin neoplasm juvenile pilocytic astrocytoma squamous cell carcinoma type 2 diabetes mellitus cervical cancer malignant mesothelioma urinary bladder neoplasm Cholestasis in newborn digestive system neuroendocrine neoplasm myopathy Emery-Dreifuss muscular dystrophy ovarian cancer Alagille syndrome due to a JAG1 point mutation psoriasis bladder benign neoplasm large cell medulloblastoma breast cancer lung carcinoma cerebral astrocytoma malignant ependymoma urinary bladder cancer chronic obstructive pulmonary disease diffuse astrocytoma Down syndrome osteogenesis imperfecta acute myeloid leukemia primitive neuroectodermal tumor astrocytoma (excluding glioblastoma) hydrocephalus bladder carcinoma in situ juvenile dermatomyositis lung benign neoplasm transitional cell carcinoma malignant glioma urinary bladder carcinoma cholestasis Crohn disease maturity-onset diabetes of the young diffuse large B-cell lymphoma Duchenne muscular dystrophy osteosarcoma pituitary cancer atypical teratoid rhabdoid tumor intellectual disability breast adenocarcinoma lung cancer cancer lymphoma

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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.