5AEJ | pdb_00005aej

Crystal structure of human Gremlin-1

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)
D	DAN	e5aejD1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: DAN	ECOD (1.6)
C	DAN	e5aejC1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: DAN	ECOD (1.6)
B	DAN	e5aejB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: DAN	ECOD (1.6)
A	DAN	e5aejA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: DAN	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.2.0)
C	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.2.0)
B	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.2.0)
A	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03045	DAN domain (DAN)	DAN domain	This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family [1] after the first member to be reported. This family includes DAN, Cerberu ...	This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family [1] after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling. It is postulated that all members of this family antagonise different TGF beta Pfam:PF00019 ligands [1]. Recent work shows that the DAN protein is not an efficient antagonist of BMP-2/4 class signals, we found that DAN was able to interact with GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GREMLIN-1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity morphogen activity receptor ligand activity signaling receptor activator activity BMP binding cytokine binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity morphogen activity receptor ligand activity signaling receptor activator activity BMP binding cytokine binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity protein kinase regulator activity kinase activator activity enzyme activator activity protein kinase activator activity kinase regulator activity identical protein binding protein homodimerization activity protein dimerization activity cytokine activity cytokine receptor binding vascular endothelial growth factor receptor binding vascular endothelial growth factor receptor 2 binding growth factor receptor binding	regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion negative regulation of leukocyte chemotaxis regulation of cell motility response to stimulus regulation of response to external stimulus negative regulation of biological process negative regulation of chemotaxis negative regulation of monocyte chemotaxis regulation of monocyte chemotaxis taxis negative regulation of cellular process regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration negative regulation of cell migration locomotion cell chemotaxis chemotaxis regulation of leukocyte chemotaxis negative regulation of response to stimulus regulation of leukocyte migration response to external stimulus regulation of chemotaxis monocyte chemotaxis leukocyte migration cellular response to chemical stimulus negative regulation of leukocyte migration negative regulation of immune system process regulation of response to stimulus immune system process regulation of locomotion response to chemical negative regulation of response to external stimulus mononuclear cell migration negative regulation of cell motility leukocyte chemotaxis signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of cell communication developmental process heart development multicellular organismal process cellular developmental process cardiac muscle tissue development cardiac muscle cell differentiation animal organ development muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development multicellular organism development cell differentiation anatomical structure development striated muscle cell differentiation muscle tissue development system development cell-cell signaling positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction positive regulation of biological process cell surface receptor protein tyrosine kinase signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus regulation of vascular endothelial growth factor signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of cellular response to vascular endothelial growth factor stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus positive regulation of vascular endothelial growth factor signaling pathway vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus response to growth factor positive regulation of signaling cell migration involved in sprouting angiogenesis blood vessel morphogenesis tube development endothelial cell migration angiogenesis sprouting angiogenesis vasculature development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel endothelial cell migration blood vessel development cell surface receptor protein serine/threonine kinase signaling pathway regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway BMP signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway response to BMP transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway collagen fibril organization extracellular matrix organization extracellular structure organization external encapsulating structure organization negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette SMAD protein signal transduction regulation of SMAD protein signal transduction negative regulation of SMAD protein signal transduction limb development appendage development negative regulation of cell population proliferation cell population proliferation osteoblast proliferation regulation of cell population proliferation negative regulation of osteoblast proliferation regulation of osteoblast proliferation cell morphogenesis regulation of developmental process bone maturation regulation of bone mineralization involved in bone maturation negative regulation of biomineral tissue development regulation of biomineral tissue development regulation of bone mineralization negative regulation of bone mineralization skeletal system development ossification biomineral tissue development regulation of multicellular organismal process ossification involved in bone maturation bone development regulation of multicellular organismal development negative regulation of developmental process bone mineralization bone mineralization involved in bone maturation developmental maturation negative regulation of bone mineralization involved in bone maturation negative regulation of ossification anatomical structure maturation negative regulation of multicellular organismal process regulation of ossification animal organ maturation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II 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 positive regulation of locomotion regulation of blood vessel endothelial cell migration positive regulation of cell migration positive regulation of cell motility regulation of endothelial cell migration positive regulation of cell migration involved in sprouting angiogenesis regulation of cell migration involved in sprouting angiogenesis positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process embryonic epithelial tube formation mesonephric epithelium development kidney epithelium development nephron morphogenesis nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development tube formation embryo development renal system development epithelial tube formation ureteric bud morphogenesis nephron tubule formation renal tubule development animal organ morphogenesis epithelial tube morphogenesis nephron development nephron epithelium development ureteric bud development morphogenesis of embryonic epithelium epithelium development mesonephric tubule formation mesonephros development embryonic morphogenesis morphogenesis of an epithelium tissue morphogenesis kidney morphogenesis mesonephric tubule morphogenesis ureteric bud formation kidney development renal tubule morphogenesis mesonephric tubule development branching morphogenesis of an epithelial tube regulation of kidney development regulation of branching involved in ureteric bud morphogenesis positive regulation of developmental process regulation of morphogenesis of a branching structure regulation of animal organ morphogenesis positive regulation of multicellular organismal process positive regulation of morphogenesis of an epithelium branching involved in ureteric bud morphogenesis regulation of morphogenesis of an epithelium regulation of anatomical structure morphogenesis morphogenesis of a branching structure positive regulation of branching involved in ureteric bud morphogenesis morphogenesis of a branching epithelium renal vesicle morphogenesis metanephric renal vesicle morphogenesis renal vesicle development epithelial cell differentiation metanephros development metanephros morphogenesis metanephric nephron development mesenchymal to epithelial transition involved in metanephros morphogenesis epithelial cell differentiation involved in kidney development mesenchymal to epithelial transition metanephric nephron morphogenesis cell differentiation involved in metanephros development cell differentiation involved in kidney development bone trabecula formation bone trabecula morphogenesis regulation of bone trabecula formation skeletal system morphogenesis negative regulation of bone trabecula formation trabecula formation trabecula morphogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of osteoblast differentiation negative regulation of osteoblast differentiation regulation of cell differentiation osteoblast differentiation negative regulation of cell differentiation regulation of localization import into cell positive regulation of cellular component organization receptor internalization transport regulation of receptor internalization vesicle-mediated transport localization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis regulation of epithelial to mesenchymal transition mesenchyme development epithelial to mesenchymal transition mesenchymal cell differentiation embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis pattern specification process regionalization dorsal/ventral pattern formation determination of bilateral symmetry determination of dorsal/ventral asymmetry determination of dorsal identity specification of symmetry positive regulation of cell population proliferation regulation of vasculature development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction cardiac muscle cell myoblast differentiation cardioblast differentiation stem cell differentiation myoblast differentiation regulation of leukocyte proliferation negative regulation of osteoclast proliferation osteoclast proliferation regulation of osteoclast proliferation leukocyte proliferation negative regulation of leukocyte proliferation regulation of cartilage development regulation of chondrocyte differentiation connective tissue development negative regulation of cartilage development negative regulation of chondrocyte differentiation chondrocyte differentiation cartilage development negative regulation of tissue remodeling negative regulation of bone remodeling regulation of bone remodeling regulation of tissue remodeling tissue remodeling bone remodeling extracellular negative regulation of signal transduction sequestering of BMP from receptor via BMP binding sequestering of extracellular ligand from receptor extracellular regulation of signal transduction proximal/distal pattern formation	cellular anatomical structure extracellular region extracellular space cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B, C, D	IPR004133	DAN	Domain
A, B, C, D	IPR017159	Gremlin-1/2	Family
A, B, C, D	IPR006207	Cystine knot, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60565	classic familial adenomatous polyposis polyposis syndrome, hereditary mixed, 1 colorectal cancer hypospadias pulmonary fibrosis Hamman-Rich syndrome idiopathic interstitial pneumonia large cell medulloblastoma lung carcinoma malignant mesothelioma astrocytic tumor medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Down syndrome classic familial adenomatous polyposis polyposis syndrome, hereditary mixed, 1 colorectal cancer hypospadias pulmonary fibrosis Hamman-Rich syndrome idiopathic interstitial pneumonia large cell medulloblastoma lung carcinoma malignant mesothelioma astrocytic tumor medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Down syndrome progressive supranuclear palsy gastric carcinoma subependymal giant cell astrocytoma genetic intestinal polyposis hereditary diffuse gastric adenocarcinoma interstitial cystitis lung adenocarcinoma malignant ependymoma atopic eczema nasopharyngeal carcinoma colorectal adenoma pancreatic ductal adenocarcinoma Pick disease congenital anomaly of kidney and urinary tract ductal breast carcinoma in situ psoriasis gastric neoplasm ulcerative colitis glioblastoma invasive ductal breast carcinoma lung cancer malignant glioma malignant pancreatic neoplasm breast cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma colorectal carcinoma pilocytic astrocytoma cystic fibrosis primitive neuroectodermal tumor gastric cancer

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.