3N1R | pdb_00003n1r

Crystal Structure of ShhN

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)
A	d3n1ra_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	Hedgehog (development protein), N-terminal signaling domain	Sonic hedgehog	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)
A	SCOP2B Superfamily	Hedgehog/DD-peptidase	8040401	3001458	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)
A	HH_signal	e3n1rA1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: HH_signal	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01085	Hedgehog amino-terminal signalling domain (HH_signal)	Hedgehog amino-terminal signalling domain	For the carboxyl Hint module, see Pfam:PF01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sonic hedgehog protein	patched binding protein binding binding signaling receptor binding catalytic activity, acting on a protein cholesterol-protein transferase activity transferase activity catalytic activity glycosaminoglycan binding carbohydrate derivative binding extracellular matrix binding laminin-1 binding laminin binding cation binding patched binding protein binding binding signaling receptor binding catalytic activity, acting on a protein cholesterol-protein transferase activity transferase activity catalytic activity glycosaminoglycan binding carbohydrate derivative binding extracellular matrix binding laminin-1 binding laminin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding calcium ion binding peptidase activity hydrolase activity	developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process biological regulation positive regulation of biological process regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process biological regulation positive regulation of biological process regulation of cell differentiation regulation of striated 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 cell differentiation positive regulation of striated muscle cell differentiation cellular process striated muscle cell differentiation positive regulation of cellular process cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway positive regulation of cerebellar granule cell precursor proliferation positive regulation of cell population proliferation regulation of cerebellar granule cell precursor proliferation cell proliferation in external granule layer cell proliferation in hindbrain system development regulation of neural precursor cell proliferation head development cell population proliferation animal organ development brain development nervous system development positive regulation of neural precursor cell proliferation central nervous system development regulation of cell population proliferation cerebellar granule cell precursor proliferation neural precursor cell proliferation hindbrain development myotube differentiation blastoderm segmentation segmentation neural crest cell development cell development mesenchyme development embryo development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation embryonic pattern specification tissue development regionalization trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation skeletal muscle cell differentiation skeletal muscle tissue development striated muscle tissue development skeletal muscle organ development skeletal muscle fiber differentiation muscle tissue development muscle organ development intein-mediated protein splicing primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process protein splicing RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process reproductive system development prostate gland development reproductive process gland development epithelial cell proliferation involved in prostate gland development urogenital system development developmental process involved in reproduction reproductive structure development epithelial cell proliferation epithelium development sclerotome development positive regulation of sclerotome development somite development regulation of sclerotome development negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion anatomical structure morphogenesis odontogenesis animal organ morphogenesis cell fate commitment regulation of localization negative regulation of sterol transport transport regulation of lipid transport negative regulation of transport organic hydroxy compound transport negative regulation of lipid localization localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport regulation of sterol transport negative regulation of lipid transport regulation of transport lipid localization lipid transport negative regulation of cholesterol transport establishment of localization regulation of lipid localization negative regulation of cholesterol efflux macromolecule localization cholesterol transport cholesterol efflux negative regulation of mesenchymal cell apoptotic process mesenchymal cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of mesenchymal cell apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death mesenchymal-epithelial cell signaling mesenchymal-epithelial cell signaling involved in prostate gland development cell-cell signaling smooth muscle cell differentiation positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation ureter smooth muscle development smooth muscle tissue development renal system development regulation of multicellular organismal process ureter smooth muscle cell differentiation tube development ureter development regulation of ureter smooth muscle cell differentiation regulation of muscle organ development positive regulation of ureter smooth muscle cell differentiation positive regulation of multicellular organismal process digestive system development hindgut morphogenesis digestive tract development tube morphogenesis digestive tract morphogenesis hindgut development salivary gland cavitation salivary gland development tube formation gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis tube lumen cavitation exocrine system development lung lobe morphogenesis respiratory tube development lung lobe development lung development respiratory system development lung morphogenesis thyroid gland development endocrine system development branching morphogenesis of an epithelial tube epithelial tube morphogenesis morphogenesis of an epithelium tissue morphogenesis morphogenesis of a branching structure epithelial tube branching involved in lung morphogenesis morphogenesis of a branching epithelium positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus positive regulation of smoothened signaling pathway regulation of smoothened signaling pathway regulation of signaling smoothened signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling tracheoesophageal septum formation heart development blood vessel morphogenesis vasculogenesis coronary vasculature development vasculature development circulatory system development vasculogenesis involved in coronary vascular morphogenesis coronary vasculature morphogenesis blood vessel development positive regulation of mesenchymal cell proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development T cell differentiation in thymus positive regulation of cell activation positive regulation of T cell differentiation in thymus T cell activation positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion leukocyte differentiation positive regulation of leukocyte cell-cell adhesion regulation of T cell differentiation in thymus lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation immune system process regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation forebrain development diencephalon development thalamus development regulation of alpha-beta T cell activation negative regulation of cell adhesion negative regulation of T cell differentiation alpha-beta T cell activation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation alpha-beta T cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of cell activation negative regulation of cell development negative regulation of immune system process negative regulation of alpha-beta T cell activation telencephalon regionalization forebrain regionalization telencephalon development animal organ formation apoptotic signaling pathway negative regulation of T cell differentiation in thymus lateral mesoderm development determination of left/right asymmetry in lateral mesoderm determination of bilateral symmetry determination of left/right symmetry left/right pattern formation mesoderm development specification of symmetry cellular component organization intermediate filament organization intermediate filament-based process organelle organization cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization intermediate filament cytoskeleton organization left lung development neurogenesis neuron differentiation generation of neurons negative regulation of neuron differentiation regulation of neuron differentiation cell fate specification protein autoprocessing negative regulation of kidney smooth muscle cell differentiation regulation of kidney smooth muscle cell differentiation negative regulation of muscle cell differentiation kidney smooth muscle cell differentiation negative regulation of smooth muscle cell differentiation cell differentiation involved in kidney development kidney smooth muscle tissue development kidney development positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process establishment of cell polarity establishment of epithelial cell polarity establishment or maintenance of cell polarity trachea development kidney mesenchymal cell proliferation metanephric mesenchyme development metanephric mesenchymal cell proliferation involved in metanephros development cell proliferation involved in kidney development kidney mesenchyme development metanephros development cell proliferation involved in metanephros development positive regulation of cell division cell division regulation of cell division establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus positive regulation of intracellular transport intracellular protein localization regulation of intracellular transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of protein localization to organelle positive regulation of transport protein transport regulation of cellular localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport positive regulation of Wnt signaling pathway regulation of Wnt signaling pathway developmental growth organ growth prostate gland epithelium morphogenesis prostate gland morphogenetic growth prostate gland growth axis elongation branch elongation of an epithelium growth developmental growth involved in morphogenesis prostate gland morphogenesis branching involved in prostate gland morphogenesis prostate epithelial cord elongation neural tube development chordate embryonic development dorsal/ventral pattern formation embryo development ending in birth or egg hatching dorsal/ventral neural tube patterning neural tube patterning catabolic process macromolecule catabolic process negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process protein catabolic process regulation of catabolic process regulation of protein catabolic process mesonephric epithelium development kidney epithelium development nephron morphogenesis nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis branching involved in ureteric bud morphogenesis renal tubule development nephron development nephron epithelium development ureteric bud development mesonephros development kidney morphogenesis mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis self proteolysis immune system development hematopoietic or lymphoid organ development thymus development bud outgrowth involved in lung branching angiogenesis sensory organ development eye development visual system development camera-type eye development sensory system development spinal cord dorsal/ventral patterning spinal cord development spinal cord patterning positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis neuron fate commitment lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation regulation of stem cell proliferation stem cell proliferation oligodendrocyte development glial cell development gliogenesis oligodendrocyte differentiation glial cell differentiation pancreas development astrocyte differentiation polarity specification of anterior/posterior axis specification of axis polarity anterior/posterior pattern specification anterior/posterior axis specification axis specification regulation of epithelial cell proliferation involved in prostate gland development positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process embryonic organ morphogenesis embryonic digestive tract morphogenesis embryonic organ development embryonic digestive tract development branching involved in salivary gland morphogenesis regulation of glial cell proliferation glial cell proliferation muscle cell proliferation skeletal muscle cell proliferation striated muscle cell proliferation thymic T cell selection negative thymic T cell selection negative T cell selection T cell selection right lung development foregut morphogenesis embryonic foregut morphogenesis mesenchymal smoothened signaling pathway involved in prostate gland development epithelial-mesenchymal signaling involved in prostate gland development epithelial-mesenchymal cell signaling myoblast differentiation regulation of dopaminergic neuron differentiation negative regulation of dopaminergic neuron differentiation dopaminergic neuron differentiation negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of leukocyte proliferation lymphocyte proliferation regulation of leukocyte proliferation mononuclear cell proliferation leukocyte proliferation negative regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of animal organ morphogenesis regulation of odontogenesis regulation of anatomical structure morphogenesis genitalia development sex differentiation male sex differentiation male genitalia development epidermis development molting cycle process hair cycle epidermis morphogenesis skin development skin epidermis development hair follicle development molting cycle hair cycle process hair follicle morphogenesis embryonic hindlimb morphogenesis hindlimb morphogenesis negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process proteasomal protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process collecting duct development metanephric collecting duct development mesenchymal cell proliferation involved in lung development branching involved in blood vessel morphogenesis regulation of mesenchymal cell proliferation involved in prostate gland development mesenchymal cell proliferation involved in prostate gland development negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound 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 biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of alpha-beta T cell activation positive regulation of alpha-beta T cell differentiation negative regulation of signaling negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction formation of anatomical boundary positive thymic T cell selection positive T cell selection regulation of reproductive process positive regulation of reproductive process positive regulation of epithelial cell proliferation involved in prostate gland development axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis 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 negative regulation of gene expression positive regulation of skeletal muscle cell proliferation regulation of skeletal muscle cell proliferation embryonic digit morphogenesis positive regulation of nervous system development regulation of neurogenesis regulation of gliogenesis regulation of astrocyte differentiation positive regulation of gliogenesis regulation of nervous system development positive regulation of neurogenesis positive regulation of astrocyte differentiation regulation of glial cell differentiation positive regulation of glial cell differentiation ectoderm development regulation of muscle tissue development positive regulation of skeletal muscle tissue development regulation of skeletal muscle tissue development positive regulation of muscle organ development positive regulation of striated muscle tissue development regulation of striated muscle tissue development positive regulation of muscle tissue development regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding neuroblast proliferation cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to metal ion response to chemical limb bud formation embryonic forelimb morphogenesis forelimb morphogenesis CD4-positive or CD8-positive, alpha-beta T cell lineage commitment T cell lineage commitment regulation of hormone levels steroid metabolic process androgen metabolic process hormone metabolic process lipid metabolic process ear development inner ear development regulation of canonical Wnt signaling pathway negative regulation of canonical Wnt signaling pathway transcription elongation by RNA polymerase II negative regulation of transcription elongation by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation artery development primary prostatic bud elongation negative regulation of ureter smooth muscle cell differentiation cell fate commitment involved in pattern specification cell differentiation in spinal cord central nervous system neuron differentiation ventral spinal cord interneuron specification ventral spinal cord interneuron differentiation neuron fate specification cell fate specification involved in pattern specification ventral spinal cord interneuron fate commitment ventral spinal cord development trachea morphogenesis skeletal system development embryonic skeletal system development regulation of immature T cell proliferation positive regulation of immature T cell proliferation positive regulation of lymphocyte proliferation regulation of immature T cell proliferation in thymus positive regulation of T cell proliferation positive regulation of leukocyte proliferation immature T cell proliferation in thymus positive regulation of mononuclear cell proliferation positive regulation of immature T cell proliferation in thymus immature T cell proliferation positive regulation of transcription by RNA polymerase II heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of heart left/right asymmetry midbrain development lung-associated mesenchyme development lung epithelium development positive regulation of mesenchymal cell proliferation involved in ureter development regulation of mesenchymal cell proliferation involved in ureter development mesenchymal cell proliferation involved in ureter development odontogenesis of dentin-containing tooth import into cell endocytosis vesicle-mediated transport epithelial cell proliferation involved in salivary gland morphogenesis spinal cord motor neuron differentiation osteoblast development ossification osteoblast differentiation Bergmann glial cell differentiation lateral sprouting from an epithelium regulation of morphogenesis of an epithelium morphogenesis of an epithelial bud regulation of morphogenesis of a branching structure morphogenesis of an epithelial fold morphogenesis of embryonic epithelium prostatic bud formation regulation of prostatic bud formation regulation of animal organ formation positive regulation of oligodendrocyte differentiation regulation of oligodendrocyte differentiation positive regulation of kidney smooth muscle cell differentiation regulation of neuroblast proliferation positive regulation of neuroblast proliferation roof of mouth development	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space cell periphery plasma membrane membrane extracellular matrix external encapsulating structure organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane Golgi apparatus nucleus nucleoplasm nuclear lumen Golgi membrane bounding membrane of organelle cell surface membrane microdomain membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001657	Hedgehog protein	Family
A	IPR006141	Intein N-terminal splicing region	PTM
A	IPR000320	Hedgehog, N-terminal signalling domain	Domain
A	IPR001767	Hedgehog protein, Hint domain	Domain
A	IPR050387	Hedgehog Signaling	Family
A	IPR036844	Hint domain superfamily	Homologous Superfamily
A	IPR009045	Peptidase M74/Hedgehog-like, zinc-binding domain superfamily	Homologous Superfamily
A	IPR003586	Hint domain C-terminal	Domain
A	IPR003587	Hint domain N-terminal	Domain

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.