6XSW

Structure of the Notch3 NRR in complex with an antibody Fab Fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6xswd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d6xswa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d6xswg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H	d6xswh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d6xswb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d6xswe_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
I	d6xswi_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
K [auth L]	d6xswl_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	C1-set_1	e6xswD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D	V-set_10	e6xswD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
A	C1-set_1	e6xswA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A	V-set_10	e6xswA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
G	C1-set_1	e6xswG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G	V-set_10	e6xswG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
H	C1-set_1	e6xswH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
H	V-set_10	e6xswH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
B	C1-set_4	e6xswB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e6xswB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E	C1-set_4	e6xswE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E	V-set	e6xswE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
I	C1-set_4	e6xswI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
I	V-set	e6xswI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
K [auth L]	C1-set_4	e6xswL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
K [auth L]	V-set	e6xswL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F	NOD	e6xswF1	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
F	Notch	e6xswF3	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)
C	NOD	e6xswC1	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
C	Notch	e6xswC3	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)
J	NOD	e6xswJ1	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
J	Notch	e6xswJ3	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)
L [auth X]	NOD	e6xswX1	A: a+b two layers	X: Alpha-beta plaits	H: Notch heterodimerization domain (From Topology)	T: Notch heterodimerization domain	F: NOD	ECOD (1.6)
L [auth X]	Notch	e6xswX3	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D, G, H	Heavy Chain	IGHV3	-	neurogenic locus notch homolog protein 3	SAbDab (2024-09-06)
B, E, I, K [auth L]	Light Chain	IGKV1	Kappa	neurogenic locus notch homolog protein 3	SAbDab (2024-09-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, J, L [auth X]	PF06816	NOTCH protein (NOD)	NOTCH protein	-	Family
C, F, J, L [auth X]	PF07684	NOTCH protein (NODP)	NOTCH protein	-	Family
C, F, J, L [auth X]	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, D, G, H	Anti-N3 Fab Heavy Chain	-	-	-
B, E, I, K [auth L]	Anti-N3 Fab Light Chain	-	-	-
C, F, J, L [auth X]	Neurogenic locus notch homolog protein 3	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity cell adhesion molecule binding cadherin binding protein binding enzyme binding identical protein binding	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation blood vessel morphogenesis tube development artery development vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis artery morphogenesis blood vessel development positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of RNA metabolic 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 nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of miRNA transcription positive regulation of cellular metabolic process positive regulation of miRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process miRNA transcription positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of miRNA transcription neuron fate commitment cell fate commitment head development forebrain development animal organ development brain development central nervous system development axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development neuroblast differentiation cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation glomerulus vasculature morphogenesis angiogenesis renal system development kidney vasculature development renal system vasculature development glomerular capillary formation nephron 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 cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II 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 cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication Notch signaling pathway signal transduction positive regulation of transcription by RNA polymerase II	cell surface cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cell surface cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane protein-containing complex receptor complex extracellular region Golgi membrane Golgi apparatus bounding membrane of organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, J, L [auth X]	IPR008297	Notch	Family
C, F, J, L [auth X]	IPR010660	Notch, NOD domain	Domain
C, F, J, L [auth X]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
C, F, J, L [auth X]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C, F, J, L [auth X]	IPR000800	Notch domain	Domain
C, F, J, L [auth X]	IPR024600	Notch, C-terminal	Domain
C, F, J, L [auth X]	IPR013032	EGF-like, conserved site	Conserved Site
C, F, J, L [auth X]	IPR000742	EGF-like domain	Domain
C, F, J, L [auth X]	IPR002110	Ankyrin repeat	Repeat
C, F, J, L [auth X]	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
C, F, J, L [auth X]	IPR022331	Neurogenic locus Notch 3	Family
C, F, J, L [auth X]	IPR035993	Notch-like domain superfamily	Homologous Superfamily
C, F, J, L [auth X]	IPR050906	Notch signaling pathway	Family
C, F, J, L [auth X]	IPR011656	Notch, NODP domain	Domain
C, F, J, L [auth X]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
C, F, J, L [auth X]	IPR001881	EGF-like calcium-binding domain	Domain
C, F, J, L [auth X]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, J, L [auth X]	Pharos: Q9UM47	lateral meningocele syndrome glioblastoma CARASIL syndrome non-small cell lung carcinoma cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 esophageal squamous cell carcinoma infantile myofibromatosis pancreatic ductal adenocarcinoma breast carcinoma squamous cell carcinoma giant cell glioblastoma leukodystrophy skin cancer myofibromatosis, infantile, 2 skin neoplasm lateral meningocele syndrome glioblastoma CARASIL syndrome non-small cell lung carcinoma cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 esophageal squamous cell carcinoma infantile myofibromatosis pancreatic ductal adenocarcinoma breast carcinoma squamous cell carcinoma giant cell glioblastoma leukodystrophy skin cancer myofibromatosis, infantile, 2 skin neoplasm lung cancer malignant mesothelioma malignant pancreatic neoplasm migraine disorder Alzheimer disease psoriasis Lung Neoplasms myofibromatosis, infantile, 1 atypical teratoid rhabdoid tumor cerebrovascular disorder lung benign neoplasm malignant glioma breast cancer primitive neuroectodermal tumor cystic fibrosis gastric carcinoma hepatocellular carcinoma