4YWT | pdb_00004ywt

Crystal structure of full-length glypican-1 core protein after controlled crystal dehydration to 87% relative humidity

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Frizzled domain-like	8090919	3001950	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Frizzled domain-like	8090919	3001950	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Frizzled domain-like	8090919	3001950	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Frizzled domain-like	8090919	3001950	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)
D	Glyco_hydro_31_3rd	e4ywtD1	A: alpha bundles	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (develop294)
C	Glyco_hydro_31_3rd	e4ywtC1	A: alpha bundles	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (develop294)
B	PhyH	e4ywtB1	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: PhyH	ECOD (develop294)
A	PhyH	e4ywtA1	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: PhyH	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glypican-1	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding extracellular matrix binding protein binding laminin binding fibroblast growth factor binding growth factor binding	response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway negative regulation of fibroblast growth factor receptor signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus fibroblast growth factor receptor signaling pathway regulation of cell communication cellular process response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway developmental process multicellular organismal process cellular component assembly involved in morphogenesis nervous system development myelin assembly cellular component organization cellular component biogenesis myelination anatomical structure morphogenesis multicellular organism development cellular anatomical entity morphogenesis cellular component assembly axon ensheathment ensheathment of neurons anatomical structure formation involved in morphogenesis anatomical structure development cellular component organization or biogenesis system development cellular developmental process peripheral nervous system development neurogenesis gliogenesis glial cell differentiation cell differentiation Schwann cell differentiation cell migration cell motility regulation of localization cellular localization regulation of protein localization localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization intracellular protein localization regulation of protein localization to membrane carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process heparan sulfate proteoglycan metabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process heparan sulfate proteoglycan catabolic process metabolic process protein metabolic process macromolecule metabolic process proteoglycan catabolic process proteoglycan metabolic process skeletal muscle cell differentiation regulation of developmental process skeletal muscle tissue development positive regulation of biological process regulation of cell differentiation striated muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development regulation of skeletal muscle cell differentiation positive regulation of cell differentiation positive regulation of skeletal muscle cell differentiation muscle tissue development muscle organ development positive regulation of cellular process animal organ development tissue development	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell surface cytosol cell periphery plasma membrane membrane membrane microdomain membrane raft extracellular matrix external encapsulating structure nucleus nucleoplasm nuclear lumen Golgi apparatus endomembrane system Golgi lumen side of membrane endosome intracellular vesicle cytoplasmic vesicle synapse cell junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001863	Glypican	Family
A, B, C, D	IPR019803	Glypican, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P35052	biliary atresia ABri amyloidosis cutaneous lupus erythematosus large cell medulloblastoma medulloblastoma ovarian cancer ADan amyloidosis extrahepatic biliary atresia malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia glioblastoma Malignant neoplasm of breast osteosarcoma psoriasis

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.