GO:0005600 collagen type XIII trimer: Components, Assembly and Research Methods, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0005600 collagen type XIII trimer describes a homotrimer of three alpha1(XIII) chains whose triple-helical domains span the plasma membrane.
• Trimerization depends on a short N-terminal sequence and on coiled-coil motifs that act as independent oligomerization domains.
• Disulfide-bonded trimer formation is enhanced by prolyl 4-hydroxylase, linking collagen modification to assembly.
• The type XIII collagen ectodomain forms a 150-nm rod that binds fibronectin, nidogen-2, perlecan and heparin, suggesting matrix-anchoring functions.
• Type XIII collagen belongs to the membrane-associated collagens with interrupted triple helices (MACITs), conserved from a bilaterian common ancestor.
• The term is a cellular_component annotation useful for interpreting extracellular matrix, adhesion and basement-membrane research.
Description
GO:0005600 collagen type XIII trimer is a cellular_component term describing a collagen homotrimer built from three alpha1(XIII) chains, in which type XIII collagen triple helices span the plasma membrane. Unlike fibrillar collagens that assemble into extracellular fibers, this trimer is a membrane-spanning collagenous complex, placing it at the interface between the cell surface and the extracellular matrix. Researchers encounter this term when annotating proteins that form transmembrane collagen triple helices and when studying how cells anchor matrix components at the plasma membrane. The trimer is not merely a structural curiosity: its ectodomain is a long rod capable of binding fibronectin, nidogen-2, perlecan and heparin, which positions it as a potential organizer of matrix-cell contacts. Understanding its assembly also requires attention to disulfide bonding and coiled-coil motifs, because these features govern how the three chains come together. Because the term is defined by chain composition and membrane-spanning topology, it is best studied with methods that resolve oligomeric state, disulfide connectivity and membrane association.
collagen type XIII trimer At A Glance
| GO ID | GO:0005600 |
|---|---|
| GO term | collagen type XIII trimer |
| Ontology | cellular_component |
| Synonym | none |
| Definition | A collagen homotrimer of alpha1(XIII) chains; type XIII collagen triple helices span the plasma membrane. |
| Major function | Membrane-spanning collagen trimer that can bind extracellular matrix ligands such as fibronectin, nidogen-2, perlecan and heparin. |
| Chain composition | Homotrimer of three alpha1(XIII) chains. |
| Assembly features | Trimerization requires a short N-terminal sequence and involves coiled-coil motifs and disulfide bonds. |
| Related protein family | Membrane-associated collagens with interrupted triple helices (MACITs). |
What Is GO:0005600?
In plain terms, GO:0005600 collagen type XIII trimer is a three-chain collagen complex made only of alpha1(XIII) chains, and its triple-helical regions cross the plasma membrane. The QuickGO definition emphasizes two features: it is a homotrimer, meaning all three chains are the same type XIII collagen polypeptide, and its triple helices span the plasma membrane rather than remaining entirely extracellular. This distinguishes it from soluble or fibrillar collagen trimers and makes it a membrane-associated collagen assembly.
Why Is collagen type XIII trimer Important in Cell Biology?
GO:0005600 is important because it captures a distinct class of collagen assembly that is integrated into the plasma membrane rather than deposited only in the extracellular space. This membrane-spanning architecture allows type XIII collagen to connect intracellular and extracellular environments, and its ectodomain can interact with matrix proteins such as fibronectin, nidogen-2, perlecan and heparin. For researchers, the term provides a precise annotation target when studying transmembrane collagens, disulfide-dependent oligomerization and coiled-coil-mediated assembly. It also offers an evolutionary anchor, since MACITs including type XIII collagen trace to a bilaterian common ancestor and show functional conservation.
• Defines a membrane-spanning collagen trimer rather than a purely extracellular collagen fiber.
• Links collagen biochemistry to plasma membrane biology and cell-matrix adhesion.
• Highlights disulfide-bonded trimer assembly enhanced by prolyl 4-hydroxylase.
• Identifies coiled-coil motifs as independent oligomerization domains in transmembrane collagens.
• Provides a model for studying N-terminal sequences required for trimerization.
• Supports annotation of MACIT family proteins across species.
• Helps interpret interactions with fibronectin, nidogen-2, perlecan and heparin.
• Useful for extracellular matrix and basement-membrane research programs.
What Happens During collagen type XIII trimer?
Chain synthesis and N-terminal trimerization signal
In simple terms: The cell makes type XIII collagen chains, and a short region near their start helps them find each other.
Type XIII collagen trimer formation depends on a short sequence in the N-terminal region that is required for trimerization and is conserved in other collagenous transmembrane proteins. This signal ensures that the three alpha1(XIII) chains can associate before or during triple-helix formation, which is a prerequisite for the membrane-spanning trimer described by GO:0005600.
Coiled-coil mediated oligomerization
In simple terms: Special spiral-shaped regions act like Velcro to hold the chains together.
Type XIII collagen and some other transmembrane collagens contain two separate coiled-coil motifs that may function as independent oligomerization domains. These motifs provide distinct interaction surfaces for chain recognition and assembly, helping explain how a homotrimer of alpha1(XIII) chains is built.
Disulfide bonding and prolyl 4-hydroxylase enhancement
In simple terms: Chemical cross-links stabilize the trimer, and an enzyme that modifies collagen makes this stabilization better.
Type XIII collagen forms homotrimers with three triple-helical collagenous domains, and its association into disulfide-bonded trimers is enhanced by prolyl 4-hydroxylase. Disulfide bonds and alpha-helical coiled-coils both contribute to the biosynthesis of type XIII collagen and other collagenous transmembrane proteins. This means the assembly pathway couples collagen hydroxylation to covalent stabilization of the trimer.
Membrane insertion and ectodomain rod formation
In simple terms: The finished trimer sits in the cell membrane and projects a long arm outward.
The type XIII collagen ectodomain is a 150-nm rod and is capable of binding to fibronectin, nidogen-2, perlecan, and heparin. Because the triple helices span the plasma membrane, the trimer can present this rod to the extracellular environment while retaining a membrane anchor, consistent with the GO:0005600 definition.
Evolutionary conservation of MACIT assembly
In simple terms: This kind of membrane collagen is ancient and has been kept through evolution.
Membrane-associated collagens with interrupted triple-helices (MACITs) evolved from a bilaterian common ancestor and show functional conservation in C. elegans. Type XIII collagen is part of this family, so the trimer assembly principles described for it are likely to reflect conserved mechanisms across metazoans.
Key Genes Involved in GO:0005600 collagen type XIII trimer
The genes and proteins most directly relevant to GO:0005600 include the type XIII collagen alpha1 chain, enzymes and motifs that control its assembly, and extracellular ligands of its ectodomain.
| Gene | Major Role | Research Relevance |
|---|---|---|
| COL13A1 | Encodes the alpha1(XIII) chain that forms the homotrimer | Core component of GO:0005600; required for trimer definition |
| P4HB | Prolyl 4-hydroxylase subunit that enhances disulfide-bonded trimer formation | Modifies collagen and supports assembly |
| COL4A1 | Another collagenous transmembrane/network collagen used in comparative studies | Helps define MACIT and collagen assembly principles |
| COL17A1 | Transmembrane collagen with coiled-coil motifs | Comparative model for oligomerization domains |
| FN1 | Fibronectin ligand of the type XIII collagen ectodomain | Matrix interaction partner in binding assays |
| NID2 | Nidogen-2 ligand of the type XIII collagen ectodomain | Basement membrane interaction partner |
| HSPG2 | Perlecan ligand of the type XIII collagen ectodomain | Proteoglycan interaction partner |
| COL13A1 N-terminal region | Short sequence required for trimerization | Defines the trimerization signal |
| Coiled-coil motif 1 | Independent oligomerization domain | Assembly mechanism research |
| Coiled-coil motif 2 | Independent oligomerization domain | Assembly mechanism research |
| Disulfide-bonded trimers | Covalent stabilization of the homotrimer | Biogenesis and secretion studies |
| Triple-helical collagenous domains | Three triple-helical regions in type XIII collagen | Structural basis of membrane-spanning collagen |
| MACIT family proteins | Membrane-associated collagens with interrupted triple helices | Evolutionary and functional comparison |
| C. elegans MACIT orthologs | Conserved MACIT function | Model organism validation |
| Prolyl 4-hydroxylase complex | Enzyme complex that enhances trimer association | Collagen modification and assembly |
| Heparin-binding site | Ectodomain interaction with heparin | Matrix ligand binding studies |
How Is collagen type XIII trimer Regulated?
Type XIII collagen trimer assembly is regulated at the level of chain modification and oligomerization. Prolyl 4-hydroxylase enhances association into disulfide-bonded trimers, linking collagen hydroxylation to covalent stabilization. Disulfide bonds and alpha-helical coiled-coils both contribute to the biosynthesis of type XIII collagen and other collagenous transmembrane proteins, indicating that redox state and coiled-coil integrity influence assembly. In addition, a short N-terminal sequence is required for trimerization and is conserved in other collagenous transmembrane proteins, suggesting a dedicated regulatory element for chain recognition. The presence of two separate coiled-coil motifs that may function as independent oligomerization domains further implies modular regulation of assembly.
collagen type XIII trimer and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| COL13A1 | Collagen assembly and matrix interaction biology | COL13A1 knockout cell model |
| COL13A1 | Trimerization signal dysfunction | Point mutation at N-terminal trimerization sequence |
| P4HB | Collagen modification and disulfide-bonded trimer enhancement | P4HB knockdown or knockout cells |
| FN1 | Matrix ligand binding by type XIII collagen ectodomain | Recombinant ectodomain binding assays |
| NID2 | Basement membrane interaction | Nidogen-2 binding and co-culture models |
Collagen assembly defects and matrix biology
Because GO:0005600 describes a membrane-spanning collagen trimer, defects in its assembly would be expected to affect collagen biosynthesis and matrix interactions. Type XIII collagen trimer formation depends on N-terminal trimerization signals, coiled-coil motifs and disulfide bonding, all of which are required for normal biosynthesis of collagenous transmembrane proteins. The ectodomain binds fibronectin, nidogen-2, perlecan and heparin, so altered trimer levels could influence basement-membrane and matrix organization.
Factor XIII and Crohn's disease: a cautionary nomenclature note
The term collagen type XIII trimer refers to collagen XIII, not coagulation factor XIII. Studies of diminished factor XIII in Crohn's disease concern a different protein and should not be conflated with GO:0005600. This distinction matters for literature searches and for correct annotation of collagen XIII biology.
Evolutionary conservation and model organisms
MACITs, including type XIII collagen, evolved from a bilaterian common ancestor and show functional conservation in C. elegans. This conservation supports the use of invertebrate and vertebrate models to study the trimer and to infer disease relevance from conserved assembly mechanisms.
From collagen type XIII trimer-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Is COL13A1 required for collagen type XIII trimer formation? | COL13A1 knockout cell line |
| Which N-terminal residues are required for trimerization? | Point-mutation knock-in of the N-terminal trimerization sequence |
| How do coiled-coil motifs contribute to oligomerization? | Coiled-coil deletion or point-mutation models |
| Where does the trimer localize in cells? | Tagged knock-in of COL13A1 with a fluorescent or epitope tag |
| Does excess type XIII collagen alter matrix binding? | COL13A1 overexpression cell model |
| Is prolyl 4-hydroxylase required for disulfide-bonded trimer assembly? | P4HB knockout or overexpression models |
How to Study the collagen type XIII trimer Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Non-reducing SDS-PAGE | Disulfide-bonded trimer versus monomer | Assessing type XIII collagen assembly |
| Reducing SDS-PAGE | Total chain pool after disulfide reduction | Comparing assembly efficiency |
| Solid-phase binding assay | Interaction with fibronectin, nidogen-2 or perlecan | Mapping ectodomain ligands |
| Heparin affinity assay | Heparin binding by the ectodomain | Characterizing matrix interactions |
| Fluorescence microscopy | Cellular localization of tagged collagen XIII | Membrane-spanning trimer imaging |
| Coiled-coil prediction and mutagenesis | Oligomerization domain function | Testing coiled-coil motifs |
| Prolyl 4-hydroxylase manipulation | Effect of hydroxylation on trimer formation | Assembly regulation studies |
| Cross-species sequence comparison | Conservation of MACIT assembly features | Evolutionary annotation |
Biochemical analysis of trimer assembly
Non-reducing and reducing gel electrophoresis can distinguish disulfide-bonded trimers from monomers, which is central to studying type XIII collagen biosynthesis. These methods directly test the assembly state described by GO:0005600 and can be combined with prolyl 4-hydroxylase manipulation.
Binding assays for ectodomain ligands
The type XIII collagen ectodomain binds fibronectin, nidogen-2, perlecan and heparin, so solid-phase binding assays and heparin affinity methods can define its interaction profile. Such assays connect the trimer to extracellular matrix function and help validate candidate partners.
Imaging of membrane-spanning collagen
Because the trimer spans the plasma membrane, imaging approaches that resolve membrane and extracellular domains are appropriate for localization studies. The 150-nm rod length of the ectodomain provides a measurable structural feature for microscopy and structural analysis.
Comparative and evolutionary analysis
Sequence and functional comparison across MACIT family members and model organisms can identify conserved assembly determinants. This is useful when direct experimental data for a specific motif are limited.
How CRISPR Can Be Used to Study GO:0005600 collagen type XIII trimer
Knockout
CRISPR knockout of COL13A1 can eliminate the alpha1(XIII) chain and test whether the collagen type XIII trimer is required for matrix interactions or membrane-associated collagen functions. Knockout of P4HB can separately test the role of prolyl 4-hydroxylase in enhancing disulfide-bonded trimer formation.
Point Mutation
Point mutations can be introduced into the short N-terminal sequence required for trimerization to define which residues are essential. Similarly, mutations in coiled-coil motifs can test their proposed function as independent oligomerization domains.
Knock-in
Tagged knock-in of COL13A1 allows visualization of the membrane-spanning trimer and its ectodomain in cells. Knock-in of disease-relevant or assembly-relevant variants can also be used to study disulfide bonding and triple-helix formation.
Overexpression
Overexpression of COL13A1 can test whether excess type XIII collagen alters trimer formation, secretion or binding to fibronectin, nidogen-2, perlecan and heparin. Overexpression of prolyl 4-hydroxylase subunits can test enhancement of disulfide-bonded trimer assembly.
How EDITGENE Supports collagen type XIII trimer Research
Researchers studying collagen type XIII trimer-related genes often need to determine whether a candidate gene is causally involved in trimer assembly, membrane localization or matrix binding. EDITGENE provides CRISPR-based cell models and screening services that allow such questions to be tested directly in relevant cell backgrounds.
Contact EDITGENE today to design your custom CRISPR model for collagen type XIII trimer research.
Frequently Asked Questions About collagen type XIII trimer
What is GO:0005600 collagen type XIII trimer?
GO:0005600 is a cellular_component term for a homotrimer of three alpha1(XIII) collagen chains whose triple helices span the plasma membrane.
What genes are involved in collagen type XIII trimer?
The core gene is COL13A1, which encodes the alpha1(XIII) chain; modifying enzymes such as prolyl 4-hydroxylase and ligands such as fibronectin, nidogen-2 and perlecan are also relevant.
How is collagen type XIII trimer assembled?
Assembly requires a short N-terminal trimerization sequence, coiled-coil motifs and disulfide bonding, with prolyl 4-hydroxylase enhancing disulfide-bonded trimer formation.
Is collagen type XIII trimer the same as factor XIII?
No. Collagen type XIII is a transmembrane collagen, whereas factor XIII is a coagulation protein studied in conditions such as Crohn's disease.
What does the type XIII collagen ectodomain bind?
The ectodomain is a 150-nm rod that binds fibronectin, nidogen-2, perlecan and heparin.
Why is collagen type XIII trimer important in matrix biology?
Because it spans the plasma membrane and binds matrix ligands, it can connect cells to the extracellular matrix.
What are MACITs?
MACITs are membrane-associated collagens with interrupted triple helices; type XIII collagen belongs to this family, which evolved from a bilaterian common ancestor.
How can I study collagen type XIII trimer in the lab?
Common approaches include non-reducing gels for disulfide-bonded trimers, binding assays for ectodomain ligands, imaging of tagged collagen XIII and CRISPR knockout or point-mutation models.
Does prolyl 4-hydroxylase affect collagen type XIII trimer?
Yes, association into disulfide-bonded trimers is enhanced by prolyl 4-hydroxylase.
What CRISPR models are useful for collagen type XIII trimer research?
COL13A1 knockout, point mutation of the N-terminal trimerization sequence, tagged knock-in and overexpression models are all useful.
Conclusion
GO:0005600 collagen type XIII trimer defines a membrane-spanning homotrimer of alpha1(XIII) chains with distinctive assembly requirements, including an N-terminal trimerization sequence, coiled-coil motifs and disulfide bonding enhanced by prolyl 4-hydroxylase. Its ectodomain forms a 150-nm rod that binds fibronectin, nidogen-2, perlecan and heparin, linking it to matrix biology. As a conserved MACIT family member, it provides a useful model for transmembrane collagen assembly and function.
References
- 1. Snellman A et al.. 2000. Type XIII collagen forms homotrimers with three triple helical collagenous domains and its association into disulfide-bonded trimers is enhanced by prolyl 4-hydroxylase.. J Biol Chem 275(12):8936-44 PMID: 10722741
- 2. Latvanlehto A et al.. 2003. Type XIII collagen and some other transmembrane collagens contain two separate coiled-coil motifs, which may function as independent oligomerization domains.. J Biol Chem 278(39):37590-9 PMID: 12832406
- 3. Snellman A et al.. 2007. The role of disulfide bonds and alpha-helical coiled-coils in the biosynthesis of type XIII collagen and other collagenous transmembrane proteins.. J Biol Chem 282(20):14898-905 PMID: 17344215
- 4. Tu H et al.. 2002. The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin.. J Biol Chem 277(25):23092-9 PMID: 11956183
- 5. Snellman A et al.. 2000. A short sequence in the N-terminal region is required for the trimerization of type XIII collagen and is conserved in other collagenous transmembrane proteins.. EMBO J 19(19):5051-9 PMID: 11013208
- 6. Chamouard P et al.. 1998. Significance of diminished factor XIII in Crohn's disease.. Am J Gastroenterol 93(4):610-4 PMID: 9576457
- 7. Tu H et al.. 2015. Membrane-associated collagens with interrupted triple-helices (MACITs): evolution from a bilaterian common ancestor and functional conservation in C. elegans.. BMC Evol Biol 15:281 PMID: 26667623
