HOXD13 domain architecture (UniProt P35453)
also called HOXD13 · Homeobox protein Hox-D13 · HOX4I
HOXD13 is the partner protein in the NUP98::HOXD13 fusion. Almost all of it is unstructured except one small DNA-gripping module near the end, and that module is what the fusion keeps.
The same thing, for a scientist
Reference domain architecture for HOXD13 (UniProt P35453, 343 aa). The only folded feature UniProt annotates is the **homeobox DNA-binding domain at 276-335**; the rest is largely disordered, with annotated disordered regions at 1-28 and 78-115. That architecture is why 'the fusion retains the homeodomain' is a nearly complete structural description of the 3' half of NUP98::HOXD13. Created so the 3D fusion viewer can resolve `fusion-nup98-hoxd13`, whose lane previously had no coordinates for the 3' partner.
This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.
I have never read one of these pictures before
A protein is one long chain of amino acids that folds up. The ribbon traces that chain from one end to the other; it is not a wire, it is a simplification of where the backbone runs. Drag to rotate, scroll to zoom.
Domains are the stretches of chain that do a particular job, and they are what the coloured blocks above the picture mark out. Click one and the view flies to it. In this project the important question about any domain is usually whether the fusion still has it — the labels say lost where it does not.
Anything in yellow sticks is a bound small molecule, which is usually the drug.
How this accession was resolved
UniProt's gene_exact: search matches synonyms, so a search hit is not proof of identity. This entry was built by fetching https://rest.uniprot.org/uniprotkb/P35453.json directly and reading back the primary gene name from genes[0].geneName.value (HOXD13) and the length from sequence.length (343 aa), then copying every feature boundary out of the same fetched record 1.
The sole UniProt gene-name synonym is HOX4I, a legacy symbol worth including in any literature sweep.
| uniprot | P35453 |
|---|---|
| gene symbol | HOXD13 |
| length AA | 343 |
| protein name | Homeobox protein Hox-D13 |
| alphafold ID | AF-P35453-F1 |
| resolution note | Fetched from the UniProt REST API this session; primary gene name asserted from genes[0].geneName.value, not from a gene_exact search, which matches synonyms. |
uniprot gene name synonyms
[ "HOX4I" ]
domains
[
{
"name": "Homeodomain",
"start": 276,
"end": 335,
"feature_type": "DNA binding",
"note": "UniProt feature call, fetched this session.",
"boundary_precision": "firm"
}
]disordered regions
[
{
"start": 1,
"end": 28
},
{
"start": 78,
"end": 115
}
]- Drawing a domain map implies the domains are what matter; in at least one NUP98 partner the annotated enzymatic domain was a passenger and a short unannotated interaction stretch did the work, so a tidy lane can mislead about mechanism.
- Which residue of HOXD13 does the patient fusion breakpoint fall on? The founding reports describe the junction at exon or domain level, not residue level.
- Are any of these domains dispensable for transformation in the fusion context? No separation-of-function mutant of this partner has been reported within the fusion.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
HOXD13 is UniProt P35453, 343 aa (Homeobox protein Hox-D13), with the domain boundaries listed in data.domains.
UniProtKB entry P35453, Homeobox protein Hox-D13 (HOXD13) · UniProt Consortium · UniProtKB 2026What this evidence cannot show
Primary gene name and sequence length were read back from the fetched record rather than assumed from a search result. UniProt feature boundaries are curated from primary literature of varying age and are revised; they are reference coordinates for drawing, not experimental measurements of this fusion.
Evidence that argues against this (2)
- A single annotated folded domain in a 343-residue protein means the viewer lane will be almost entirely empty, which is an honest depiction of the architecture rather than missing data - but a reader may mistake sparseness for incompleteness. Raza-Egilmez SZ et al. 1998
- Germline HOXD13 mutations cause synpolydactyly, so the protein has substantial developmental function outside haematopoiesis; a domain map says nothing about which of those functions the fusion co-opts, and the homeodomain is shared with every other HOX protein. Lin YW et al. 2005
- part of →NUP98::HOXD13, t(2;11)(q31;p15) — the myelodysplasia fusion, and a warning against targeting p53
3' partner coordinates for the fusion viewer lane
- related to →NUP98 — domain architecture and residue coordinates (with the 1817/920 numbering trap resolved)
the two halves of NUP98::HOXD13