Thrombospondin-3 (THBS3/TSP3) is a pentameric matricellular glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. It binds to extracellular matrix proteins including fibrinogen, fibronectin, laminin, and type V collagen. THBS3 contains calcium-binding type 3 repeats, EGF-like domains, and a unique EGD motif (instead of the canonical RGD integrin-binding motif found in other thrombospondins). The protein is involved in skeletal development, regulating bone maturation and epiphyseal ossification. THBS3 is also a developmentally regulated heparin-binding protein expressed in cartilage, lung, gut, and CNS during embryogenesis. Within the thrombospondin family it is classified as a Group B (pentameric) thrombospondin together with THBS4 and THBS5/COMP, and in developing bone it localizes to the growth plate proliferating zone and perichondrium. Beyond the skeleton, more recent work implicates THBS3 in damage-responsive matricellular signaling: it has been reported to bind ATF6alpha and activate ER stress and to modulate integrin signaling in cardiac stress, to act as a pseudorabies virus coreceptor by binding viral glycoprotein D in cell-based assays, and (in a preprint) to promote cartilage catabolism and vascularization in osteoarthritis via TGF-beta/Smad signaling.
Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
Justification: THBS3's matricellular role belongs in this biological process rather than being captured as a molecular function structural constituent of the ECM (GO:0005201). As a matricellular protein, THBS3 modulates and organizes the extracellular matrix and cell-matrix interactions rather than serving as a load-bearing structural scaffold. GO:0030198 (extracellular matrix organization) is an existing GO BP term; this entry frames it as a proposed reannotation to replace the cross-aspect MF over-annotation (GO:0005201, marked MARK_AS_OVER_ANNOTATED above).
Parent term: extracellular matrix organization
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0031012 extracellular matrix | IBA GO_REF:0000033 | ACCEPT | Summary: THBS3 is a matricellular protein that localizes to and functions within the extracellular matrix. This is well-supported by its classification as a thrombospondin family member and its documented binding to ECM components [PMID:8288588, UniProt P49746]. Reason: Thrombospondins are canonical ECM proteins. THBS3 mediates cell-matrix interactions by binding fibrinogen, fibronectin, laminin, and type V collagen [UniProt P49746]. Proteomic studies confirm THBS3 in stem cell-derived ECM [PMID:28327460]. IBA is appropriate for this conserved family-level localization. Supporting Evidence: PMID:8288588 Metabolic labeling and immunoprecipitation analysis of cells transfected with a TSP3 expression vector revealed it to be an oligomeric heparin binding protein present in both the cell layer and medium file:human/THBS3/THBS3-deep-research-perplexity.md The primary function of THBS3 is to serve as a matricellular protein - a classification describing proteins that associate with the extracellular matrix and regulate cell-matrix interactions file:human/THBS3/THBS3-deep-research-falcon.md THBS3 encodes thrombospondinβ3 (TSP3), a secreted matricellular extracellular-matrix (ECM) glycoprotein in the thrombospondin family |
| GO:0005509 calcium ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: THBS3 contains multiple calcium-binding type 3 repeats (8 TSP type-3 repeats) and EGF-like calcium-binding domains that coordinate calcium ions, regulating protein conformation and ligand accessibility. Reason: UniProt documents multiple EGF-like calcium-binding domains and type 3 repeats that bind calcium [UniProt P49746]. The deep research indicates thrombospondins bind 10-12 calcium ions per subunit with moderate affinity (Kd ~0.1 mM) [PMID:7558000]. Calcium binding is essential for proper protein structure and function. Supporting Evidence: PMID:7558000 This region corresponds to seven type III (Ca(2+)-binding) repeats, a feature shared with other thrombospondins file:human/THBS3/THBS3-deep-research-perplexity.md Thrombospondins have been shown to bind 10-12 calcium ions per subunit with high cooperativity and moderate affinity (average Kd approximately 0.1 mM) file:human/THBS3/THBS3-deep-research-falcon.md Group B thrombospondins are described as pentameric extracellular proteins with calcium-binding architecture that supports multivalent ECM/receptor interactions |
| GO:0005576 extracellular region | IEA GO_REF:0000002 | ACCEPT | Summary: THBS3 is a secreted glycoprotein that functions in the extracellular space, consistent with its signal peptide and ECM function. Reason: UniProt confirms a signal peptide (residues 1-22) directing THBS3 to the secretory pathway [UniProt P49746]. The protein is found in the extracellular medium [PMID:8288588] and functions as a matricellular protein in the ECM. This broader term encompasses the more specific ECM localization. Supporting Evidence: PMID:8288588 Metabolic labeling and immunoprecipitation analysis of cells transfected with a TSP3 expression vector revealed it to be an oligomeric heparin binding protein present in both the cell layer and medium file:human/THBS3/THBS3-deep-research-falcon.md a secreted matricellular extracellular-matrix (ECM) glycoprotein |
| GO:0007155 cell adhesion | IEA GO_REF:0000120 | ACCEPT | Summary: THBS3 mediates cell-to-cell and cell-to-matrix adhesion as a core function of the thrombospondin family. Reason: UniProt states THBS3 is an "Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions" [UniProt P49746]. This is a fundamental property of thrombospondin family members. The protein contains integrin-binding regions (albeit EGD rather than RGD) that modulate cell adhesion. Supporting Evidence: file:human/THBS3/THBS3-deep-research-perplexity.md Thrombospondin-3 functions fundamentally as an adhesive glycoprotein that mediates critical interactions between cells and the extracellular matrix, as well as between adjacent cells file:human/THBS3/THBS3-deep-research-falcon.md Thrombospondins are multidomain, calcium-binding extracellular proteins that operate at the cell-matrix interface, affecting cell-ECM and cell-cell interactions |
| GO:0008201 heparin binding | IEA GO_REF:0000120 | ACCEPT | Summary: THBS3 is established as a heparin-binding protein through direct experimental evidence. This IEA annotation is supported by IDA evidence from the same GOA file. Reason: Direct experimental evidence demonstrates THBS3 binds heparin [PMID:8288588]. This is independently confirmed by the IDA annotation below. The IEA annotation is correct and consistent with direct assay data. Supporting Evidence: PMID:8288588 Metabolic labeling and immunoprecipitation analysis of cells transfected with a TSP3 expression vector revealed it to be an oligomeric heparin binding protein present in both the cell layer and medium |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | REMOVE | Summary: This annotation derives from a large-scale interactome study that identified protein-protein interactions for neurodegenerative disease proteins. While THBS3 likely has protein binding capacity (as an ECM glycoprotein), 'protein binding' is an uninformative term. Reason: The term 'protein binding' (GO:0005515) is too generic to be informative. PMID:32814053 is a high-throughput interactome mapping study focused on neurodegenerative disease proteins where THBS3 was incidentally identified. More specific molecular function terms (such as heparin binding, calcium ion binding, or ECM structural constituent) better describe THBS3 function. Per curation guidelines, 'protein binding' should be avoided in favor of more informative molecular function terms. Supporting Evidence: PMID:32814053 Interactome maps are valuable resources to elucidate protein function and disease mechanisms |
| GO:0003417 growth plate cartilage development | IEA GO_REF:0000107 | ACCEPT | Summary: THBS3 knockout mice show altered skeletal development including accelerated femoral epiphysis development, supporting a role in growth plate cartilage development. Reason: Mouse knockout studies demonstrate that Thbs3-null mice exhibit accelerated femoral epiphysis ossification and altered bone geometry, indicating THBS3 regulates endochondral ossification at the growth plate. This IEA annotation from ortholog data is consistent with the known developmental expression of THBS3 in cartilage [PMID:8288588]. Supporting Evidence: file:human/THBS3/THBS3-deep-research-perplexity.md Mice with a disruption of the thrombospondin 3 gene demonstrate significant differences in the geometric and biomechanical properties of bone and exhibit accelerated development of the femoral epiphysis PMID:8288588 Finally, a combination of in situ hybridization and immunocytochemistry demonstrated TSP3 to be expressed in a temporal and spatial manner during murine embryogenesis, especially in the gut, cartilage, lung, and central nervous system file:human/THBS3/THBS3-deep-research-falcon.md In developing bone, TSP3 expression is localized to the growth plate proliferating zone and perichondrium |
| GO:0043931 ossification involved in bone maturation | IEA GO_REF:0000107 | ACCEPT | Summary: THBS3 regulates skeletal maturation, with knockout mice showing accelerated bone ossification, supporting a role in controlling the rate of bone maturation. Reason: THBS3 knockout mice display altered bone biomechanical properties and accelerated femoral epiphysis ossification. The protein appears to function as a negative regulator of premature ossification during skeletal development. IEA transfer from mouse ortholog is appropriate given the high conservation of thrombospondin function. Supporting Evidence: file:human/THBS3/THBS3-deep-research-perplexity.md THBS3 has been found to be involved in the regulation of skeletal maturation, representing one of its primary developmental roles file:human/THBS3/THBS3-deep-research-falcon.md Mouse loss-of-function data summarized in review indicate TSP3 knockout causes accelerated ossification of the femoral head |
| GO:0060346 bone trabecula formation | IEA GO_REF:0000107 | UNDECIDED | Summary: THBS3 knockout mice show altered bone geometry including changes in periosteal and endocortical diameters, consistent with effects on trabecular bone formation. Reason: The available Thbs3-null mouse evidence is cortical-geometry only: increased periosteal and endocortical diameters, greater cortical moments of inertia, and increased femur bending strength. These are all measures of CORTICAL (periosteal/endocortical) bone, not trabecular bone. None of the cited evidence demonstrates an effect on trabecular bone formation (e.g. trabecular number, thickness, or spacing) specifically. Because the term GO:0060346 (bone trabecula formation) requires evidence about the trabecular compartment, which is not provided by the cortical-geometry phenotypes cited here, this annotation cannot be accepted or confidently rejected and is marked UNDECIDED pending trabecular-specific data. Supporting Evidence: file:human/THBS3/THBS3-deep-research-perplexity.md Specifically, homozygous null mice at young ages are heavier and exhibit femurs with increased periosteal and endocortical diameters, greater moments of inertia, and altered bone biomechanical properties file:human/THBS3/THBS3-deep-research-falcon.md transient increases in cortical moment of inertia that increase femur bending strength |
| GO:0005201 extracellular matrix structural constituent | RCA PMID:28327460 Comprehensive proteomic characterization of stem cell-derive... | MARK AS OVER ANNOTATED | Summary: THBS3 was identified in proteomic analysis of stem cell-derived ECM, supporting its presence as an ECM structural component. However, THBS3 functions primarily as a matricellular protein that modulates cell-ECM interactions rather than providing structural support. Reason: THBS3 is present in the ECM and was detected in proteomic studies of stem cell-derived matrices [PMID:28327460], but it functions as a matricellular regulator of cell-matrix interactions rather than as a structural ECM scaffold like collagens or elastin. The molecular function term "extracellular matrix structural constituent" (GO:0005201) implies a load-bearing structural role that THBS3 does not play, so this annotation is an over-annotation. THBS3's actual matricellular role in modulating and organizing the matrix is better captured as a biological process: extracellular matrix organization (GO:0030198), which is proposed separately in proposed_new_terms. Note that GO:0030198 is a BP term and cannot replace this MF annotation directly (a MODIFY within the same GO aspect is not possible here), so the structural-constituent MF is marked as over-annotated rather than modified. Supporting Evidence: PMID:28327460 By employing a proteomic approach, we were able to provide a comprehensive characterization of the molecular composition of ECM produced in vitro by bone marrow-derived MSC (Bm ECM), adipose-derived MSC (Ad ECM) and human neonatal dermal fibroblasts (Der ECM) file:human/THBS3/THBS3-deep-research-perplexity.md The primary function of THBS3 is to serve as a matricellular protein - a classification describing proteins that associate with the extracellular matrix and regulate cell-matrix interactions while not being structural components themselves file:human/THBS3/THBS3-deep-research-falcon.md affecting cell-ECM and cell-cell interactions rather than serving as purely structural ECM scaffolds |
| GO:0031012 extracellular matrix | HDA PMID:28327460 Comprehensive proteomic characterization of stem cell-derive... | ACCEPT | Summary: THBS3 was identified in ECM fractions by high-throughput proteomic analysis of stem cell-derived matrices, confirming its ECM localization. Reason: Proteomic characterization of ECM from bone marrow-derived MSCs, adipose-derived MSCs, and neonatal fibroblasts identified THBS3 as an ECM component [PMID:28327460]. This HDA annotation is consistent with the IBA annotation and the known function of THBS3 as a matricellular protein. Supporting Evidence: PMID:28327460 Here, we characterized and compared the protein composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts from different donors, employing quantitative proteomic methods |
| GO:0005576 extracellular region | TAS Reactome:R-HSA-382054 | ACCEPT | Summary: This annotation derives from Reactome pathway "PDGF binds to extracellular matrix proteins" which describes thrombospondin binding to PDGF in the ECM context. Reason: Reactome pathway R-HSA-382054 describes PDGF binding to ECM proteins including thrombospondins. This supports THBS3 localization to the extracellular region. The annotation is consistent with the established secreted nature of THBS3 and its ECM function. Supporting Evidence: Reactome:R-HSA-382054 PDGF binds to various types of collagens, thrombospondin and osteopontin; however, the major component of the matrix involved in PDGF binding is likely to be haparan sulphate |
| GO:0008201 heparin binding | IDA PMID:8288588 Thrombospondin 3 is a developmentally regulated heparin bind... | ACCEPT | Summary: Direct experimental evidence from transfection studies and immunoprecipitation demonstrates THBS3 is a heparin-binding protein. Reason: PMID:8288588 provides direct experimental evidence that THBS3 binds heparin. Cells transfected with a TSP3 expression vector produced oligomeric heparin-binding protein. This is a core molecular function of THBS3. Supporting Evidence: PMID:8288588 Metabolic labeling and immunoprecipitation analysis of cells transfected with a TSP3 expression vector revealed it to be an oligomeric heparin binding protein present in both the cell layer and medium |
| GO:0005509 calcium ion binding | NAS PMID:7558000 Structure and organization of the human thrombospondin 3 gen... | ACCEPT | Summary: The THBS3 gene structure paper describes the Ca2+-binding type III repeats characteristic of thrombospondins, supporting calcium binding activity. Reason: PMID:7558000 describes the THBS3 gene structure and specifically notes the seven type III (Ca2+-binding) repeats. While NAS, this is well-supported by the conserved domain architecture documented in UniProt showing multiple calcium-binding EGF-like domains and TSP type-3 repeats. Supporting Evidence: PMID:7558000 This region corresponds to seven type III (Ca(2+)-binding) repeats, a feature shared with other thrombospondins |
| GO:0007160 cell-matrix adhesion | NAS PMID:7558000 Structure and organization of the human thrombospondin 3 gen... | ACCEPT | Summary: The THBS3 gene paper describes thrombospondin family function in cell-matrix adhesion, though the paper itself focuses on gene structure rather than direct functional analysis. Reason: While PMID:7558000 focuses on gene structure, cell-matrix adhesion is a well-established function of thrombospondin family members. UniProt describes THBS3 as an "adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions." This more specific term (child of GO:0007155 cell adhesion) appropriately describes THBS3 function as an ECM protein. Supporting Evidence: file:human/THBS3/THBS3-deep-research-perplexity.md THBS3 has been documented to bind to fibrinogen, fibronectin, laminin, and type V collagen file:human/THBS3/THBS3-deep-research-falcon.md extracellular matricellular proteins that interact with ECM components and cell-surface proteins |
| GO:0048471 perinuclear region of cytoplasm | IDA PMID:11943589 Corneal stromal cells (keratocytes) express thrombospondins ... | KEEP AS NON CORE | Summary: PMID:11943589 examined TSP expression in corneal keratocytes and reported perinuclear immunoreactivity pattern for TSP-3 in wound repair phenotype cells. Reason: PMID:11943589 detected TSP-3 immunoreactivity in cultured keratocytes with a perinuclear pattern, consistent with ER/Golgi localization during protein synthesis and secretion. This intracellular localization represents the biosynthetic pathway rather than the primary functional localization. THBS3 is primarily an ECM protein, so perinuclear localization is a transient biosynthetic intermediate rather than the site of function. Supporting Evidence: PMID:11943589 The distribution of keratocyte TSP-2 and TSP-3 immunoreactivity had some similarities to that of TSP-1 and, like TSP-1, neither protein could be detected in the cells of the normal corneal stroma file:human/THBS3/THBS3-deep-research-perplexity.md Immunohistochemical analysis of heart sections from THBS3 transgenic mice and mice subjected to cardiac injury shows cardiomyocyte-restricted, intracellular localization of THBS3 protein that is directly coincident with the endoplasmic reticulum chaperone protein disulfide isomerase (PDI) file:human/THBS3/THBS3-deep-research-falcon.md THBS3 is upregulated in cardiac disease and can activate ER stress via binding ATF6Ξ± |
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Download this section (compressed HTML)Q: What is the precise molecular mechanism by which THBS3 affects integrin trafficking in cardiomyocytes, and how does the EGD motif contribute to this function?
Q: Does THBS3 directly interact with TGF-beta or does it affect TGF-beta signaling through indirect mechanisms?
Experiment: Direct binding assays comparing THBS3 (EGD motif) vs THBS4 (RGD motif) for integrin binding affinity
Hypothesis: The EGD motif in THBS3 has reduced integrin binding affinity compared to the RGD motif in THBS4, explaining their differential effects on integrin trafficking.
Experiment: Structure determination of THBS3 type 3 repeats to understand calcium coordination and conformational changes
Hypothesis: Calcium binding induces conformational changes in THBS3 type 3 repeats that regulate accessibility of ligand-binding sites.
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