1NPE | pdb_00001npe

Crystal structure of Nidogen/Laminin Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1npeb1	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	Laminin-type module	Laminin gamma1 chain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1npea_	All beta proteins	6-bladed beta-propeller	YWTD domain	YWTD domain	Nidogen	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	EGF/Laminin-like	8038351	3000412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EGF/Laminin-like	8038349	3000412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EGF/Laminin-like	8038350	3000412	SCOP2B (2022-06-29)
A	SCOP2 Family	YWTD domain	8024501	4003248	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YWTD domain-like	8036880	3000494	SCOP2 (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	Laminin_EGF_1	e1npeB2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_1	ECOD (1.6)
B	Laminin_EGF	e1npeB3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF	ECOD (1.6)
A	SGL_5	e1npeA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: SGL_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
A	2.120.10.30	Mainly Beta	6 Propeller	Neuraminidase	TolB, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF24973	Laminin/attractin EGF domain (EGF_LMN_ATRN)	Laminin/attractin EGF domain	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activi ...	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color [1]. It was thought to have dipeptidase activity but it was shown later to lack that activity [2]. Laminins are crucial for the formation of stable basement membranes and organising receptor complexes and cytoskeletal components. Netrins control guidance of central nervous system commissural axons and peripheral motor axons, serving as survival factors and regulating apoptosis.	Domain
B	PF00053	Laminin EGF domain (EGF_laminin)	Laminin EGF domain	This family is like Pfam:PF00008 but has 8 conserved cysteines instead of six.	Domain
A	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Laminin gamma-1 chain	glycosphingolipid binding binding sphingolipid binding lipid binding glycolipid binding carbohydrate derivative binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity structural molecule activity extracellular matrix structural constituent	developmental process multicellular organismal process epithelium development epidermal cell differentiation cellular developmental process epidermis development nervous system development tissue development epithelial cell differentiation hair cell differentiation generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation developmental process multicellular organismal process epithelium development epidermal cell differentiation cellular developmental process epidermis development nervous system development tissue development epithelial cell differentiation hair cell differentiation generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process system development cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization neuromuscular junction development receptor clustering synapse organization intracellular protein localization regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane positive regulation of cellular process membrane organization regulation of biological process postsynapse organization positive regulation of receptor clustering skeletal muscle acetylcholine-gated channel clustering biological regulation positive regulation of protein localization to membrane localization within membrane protein localization to membrane positive regulation of skeletal muscle acetylcholine-gated channel clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization anatomical structure morphogenesis animal organ development animal organ morphogenesis regulation of developmental process regulation of 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 cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion cell junction assembly cell-substrate junction assembly cell-substrate junction organization hemidesmosome assembly cellular component disassembly extracellular matrix disassembly extracellular matrix organization extracellular structure organization external encapsulating structure organization molting cycle process hair cycle epidermis morphogenesis morphogenesis of an epithelium tissue morphogenesis skin development skin epidermis development hair follicle development molting cycle hair cycle process hair follicle morphogenesis cell migration cell motility hair follicle cell proliferation cell population proliferation positive regulation of cell adhesion regulation of cell adhesion cellular response to stimulus positive regulation of cell communication regulation of integrin-mediated signaling pathway positive regulation of signal transduction response to stimulus signaling regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of integrin-mediated signaling pathway signal transduction regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development regulation of cellular component organization regulation of basement membrane organization regulation of extracellular matrix organization basement membrane organization chromatin organization	basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex laminin-511 trimer synaptic cleft basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex laminin-511 trimer synaptic cleft extracellular region neuromuscular junction synapse cell junction protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion
A	nidogen	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding extracellular matrix binding collagen binding protein-containing complex binding protein binding laminin binding proteoglycan binding carbohydrate derivative binding laminin-1 binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of 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 cell differentiation anatomical structure development positive regulation of cellular process multicellular organismal process animal organ development extracellular matrix organization renal system development glomerular basement membrane development cellular component organization glomerulus development multicellular organism development cellular component organization or biogenesis nephron development kidney development system development extracellular structure organization external encapsulating structure organization regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-substrate adhesion cellular response to stimulus positive regulation of cell communication regulation of integrin-mediated signaling pathway positive regulation of signal transduction response to stimulus signaling regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of integrin-mediated signaling pathway signal transduction regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of cellular component organization regulation of basement membrane organization regulation of extracellular matrix organization basement membrane organization	basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure extracellular region protein-containing complex protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR008211	Laminin, N-terminal	Domain
B	IPR002049	Laminin-type EGF domain	Domain
B	IPR000742	EGF-like domain	Domain
B	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
B	IPR050440	Laminin/Netrin Extracellular Matrix	Family
B	IPR000034	Laminin IV	Domain
A	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A	IPR024731	NELL2-like, EGF domain	Domain
A	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR026823	Complement Clr-like EGF domain	Domain
A	IPR006605	G2 nidogen/fibulin G2F	Domain
A	IPR003886	NIDO domain	Domain
A	IPR036857	Thyroglobulin type-1 superfamily	Homologous Superfamily
A	IPR000742	EGF-like domain	Domain
A	IPR009017	Green fluorescent protein	Homologous Superfamily
A	IPR000033	LDLR class B repeat	Repeat
A	IPR050778	Cueball_EGF_LRP_Nidogen	Unknown
A	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A	IPR000716	Thyroglobulin type-1	Domain