1U5M

Structure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1u5ma1	Small proteins	FnI-like domain	FnI-like domain	VWC domain	Collagen alpha 1(II) chain precursor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1u5ma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	VWC domain	8030391	4003922	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FnI-like domain	8042770	3000979	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)
A	VWC	e1u5mA1	A: few secondary structure elements	X: Fibronectin type I module-like (From Homology)	H: Fibronectin type I module-like	T: VWC domain-related	F: VWC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00093	von Willebrand factor type C domain (VWC)	von Willebrand factor type C domain	The high cutoff was used to prevent overlap with Pfam:PF00094.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	alpha 1 type II collagen isoform 1	protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding carbohydrate derivative binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development organic substance metabolic process organonitrogen compound metabolic process carbohydrate derivative metabolic process metabolic process developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development organic substance metabolic process organonitrogen compound metabolic process carbohydrate derivative metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process limb development appendage development limb bud formation anatomical structure morphogenesis appendage morphogenesis anatomical structure formation involved in morphogenesis limb morphogenesis cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cellular process response to stimulus signal transduction in absence of ligand negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication cellular process apoptotic process programmed cell death regulation of apoptotic signaling pathway central nervous system development nervous system development epithelium development otic vesicle development ear development sensory organ development tube development inner ear development embryonic skeletal joint development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development embryonic skeletal joint morphogenesis embryo development ending in birth or egg hatching embryonic skeletal system development animal organ morphogenesis skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis ear morphogenesis sensory organ morphogenesis inner ear morphogenesis regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process endochondral ossification replacement ossification endochondral bone morphogenesis ossification bone morphogenesis bone development cell aggregation cartilage condensation cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis supramolecular fiber organization extracellular structure organization external encapsulating structure organization heart development heart morphogenesis circulatory system development notochord development system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus sensory perception of light stimulus visual perception multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis cartilage development involved in endochondral bone morphogenesis cellular developmental process cell differentiation chondrocyte differentiation roof of mouth development anterior head development head development cellular response to BMP stimulus cellular response to endogenous stimulus response to BMP cellular response to growth factor stimulus response to endogenous stimulus response to growth factor	basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity protein-containing complex banded collagen fibril collagen trimer fibrillar collagen trimer complex of collagen trimers collagen type XI trimer supramolecular fiber supramolecular polymer basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity protein-containing complex banded collagen fibril collagen trimer fibrillar collagen trimer complex of collagen trimers collagen type XI trimer supramolecular fiber supramolecular polymer supramolecular complex collagen type II trimer membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008160	Collagen triple helix repeat	Repeat
A	IPR000885	Fibrillar collagen, C-terminal	Domain
A	IPR001007	VWFC domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P02458	Kniest dysplasia spondyloepiphyseal dysplasia congenita platyspondylic dysplasia, Torrance type Legg-Calve-Perthes disease mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis spondyloepimetaphyseal dysplasia, Strudwick type spondyloperipheral dysplasia-short ulna syndrome osteochondrodysplasia chondrosarcoma Czech dysplasia, metatarsal type Stickler syndrome, type I, nonsyndromic ocular synovitis cleft palate multiple epiphyseal dysplasia, Beighton type Stickler syndrome type 1 Kniest dysplasia spondyloepiphyseal dysplasia congenita platyspondylic dysplasia, Torrance type Legg-Calve-Perthes disease mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis spondyloepimetaphyseal dysplasia, Strudwick type spondyloperipheral dysplasia-short ulna syndrome osteochondrodysplasia chondrosarcoma Czech dysplasia, metatarsal type Stickler syndrome, type I, nonsyndromic ocular synovitis cleft palate multiple epiphyseal dysplasia, Beighton type Stickler syndrome type 1 melanoma spondyloepiphyseal dysplasia, Stanescu type osteoarthritis Arthritis, Experimental Stickler syndrome achondrogenesis type II cataract achondrogenesis hypochondrogenesis retinal detachment chondromalacia myopia otospondylomegaepiphyseal dysplasia arthritic joint disease Wagner disease cartilage disease spondyloepiphyseal dysplasia multiple epiphyseal dysplasia dysspondyloenchondromatosis hyperplasia avascular necrosis of femoral head, primary, 1 rheumatoid arthritis megaepiphyseal dwarfism Osgood-Schlatter disease osteogenesis imperfecta gastric carcinoma otospondylomegaepiphyseal dysplasia, autosomal recessive pituitary cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor avascular necrosis of femoral head, primary, 2 bone resorption disease malignant glioma Schwartz-Jampel syndrome mucopolysaccharidosis type 4 spondyloepiphyseal dysplasia tarda, X-linked cutaneous melanoma spondylometaphyseal dysplasia, Kozlowski type Ehlers-Danlos syndrome familial avascular necrosis of femoral head glioblastoma autosomal dominant rhegmatogenous retinal detachment X-linked mixed deafness with perilymphatic gusher large cell medulloblastoma prostate carcinoma lung cancer medulloblastoma Melnick-Needles syndrome spondyloepiphyseal dysplasia with congenital joint dislocations spondylometaphyseal dysplasia, 'corner fracture' type spondylometaphyseal dysplasia, Schmidt type osteoarthritis susceptibility 1 osteochondrosis otospondylomegaepiphyseal dysplasia, autosomal dominant pilocytic astrocytoma intellectual disability malignant ependymoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.