Oncofusion

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Proteinstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.king

NTRK3 (TrkC neurotrophin receptor) domain architecture

also called NTRK3 · TrkC neurotrophin receptor

NTRK3 is the 3' partner of ETV6::NTRK3. This entry lists where each of its functional parts sits along the protein, measured as residue numbers, so the fusion diagrams can draw which parts survive the break and which are thrown away.

The same thing, for a scientist

Reference domain architecture for NTRK3 (UniProt Q16288, 839 aa). A receptor tyrosine kinase. The kinase domain occupies 538-839, the whole C-terminal third of the protein, behind an extracellular leucine-rich-repeat and Ig-like ectodomain. Created so the 3D fusion viewer can resolve fusion-etv6-ntrk3, which previously had no coordinates for this partner and silently dropped the lane. Domain fate in the fusion is asserted by the fusion entry, not here.

What it looks like
NT-3 growth factor receptor839 aa
LRR 1 · residues 104–125 · UniProt functional region, not a fold boundary. Soft edges; render as low confidence.LRR 2 · residues 128–149 · UniProt functional region, not a fold boundary. Soft edges; render as low confidence.LRRCLRRCT · residues 160–209 · UniProt folded-domain call.Ig-like C2-type 1Ig-like C2-type 1 · residues 210–300 · UniProt folded-domain call.Ig-like C2-type 2Ig-like C2-type 2 · residues 309–382 · UniProt folded-domain call.Protein kinaseProtein kinase · residues 538–839 · UniProt folded-domain call.0200400600800
loading AF-Q16288-F1…
AlphaFold AF-Q16288-F1 ↗
colourshape

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.

very high (90+)confident (70–90)low (50–70)very low (<50)
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.

Go deeper
Why this entry exists

The join checker reported fusion-etv6-ntrk3: no protein entry for NTRK3. Without coordinates the comparative 3D viewer cannot draw the lane at all, and it was omitting it without warning rather than flagging it. This is a reference-coordinate entry: it asserts the architecture and nothing about the fusion.

Folded domains versus functional regions. UniProt mixes two very different annotation kinds. Domain, Zinc finger and DNA binding are fold calls with real boundaries. Region is a functional assertion that often spans disorder and can overlap other regions or run for hundreds of residues. Both are recorded with boundary_precision marking which is which, because drawing a soft functional region as a crisp box is exactly the kind of false precision this graph exists to avoid.

Architecture
PartResiduesKindPrecision
LRR 1104-125Repeatsoft
LRR 2128-149Repeatsoft
LRRCT160-209Domainfirm
Ig-like C2-type 1210-300Domainfirm
Ig-like C2-type 2309-382Domainfirm
Protein kinase538-839Domainfirm

5 PDB entries reference this protein.

Facts and figures
uniprotQ16288
gene symbolNTRK3
length AA839
protein nameNT-3 growth factor receptor
alphafold IDAF-Q16288-F1
n PDB total5
uniprot verifiedtrue
accession resolutionexact gene-name search, reviewed human only, gene symbol confirmed in the response
created forfusion-etv6-ntrk3
domains
LRR 1104.0LRR 1: 104LRR 2128.0LRR 2: 128LRRCT160.0LRRCT: 160Ig-like C2-type 1210.0Ig-like C2-type 1: 210Ig-like C2-type 2309.0Ig-like C2-type 2: 309Protein kinase538.0Protein kinase: 538
domains — the numbers behind the chart
[
  {
    "name": "LRR 1",
    "start": 104,
    "end": 125,
    "feature_type": "Repeat",
    "note": "UniProt functional region, not a fold boundary. Soft edges; render as low confidence.",
    "boundary_precision": "soft"
  },
  {
    "name": "LRR 2",
    "start": 128,
    "end": 149,
    "feature_type": "Repeat",
    "note": "UniProt functional region, not a fold boundary. Soft edges; render as low confidence.",
    "boundary_precision": "soft"
  },
  {
    "name": "LRRCT",
    "start": 160,
    "end": 209,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "Ig-like C2-type 1",
    "start": 210,
    "end": 300,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "Ig-like C2-type 2",
    "start": 309,
    "end": 382,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "Protein kinase",
    "start": 538,
    "end": 839,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  }
]
PDB IDS
[
  "1WWC",
  "3V5Q",
  "4YMJ",
  "6KZC",
  "6KZD"
]
How this could bite us back
  • Nothing here licenses targeting any part of NTRK3. These are coordinates, not a druggability claim; a domain with crisp boundaries is not thereby a ligandable pocket.
  • Drawing UniProt `Region` features as boxes in the viewer risks implying structural knowledge that does not exist. They are marked soft and should be rendered differently from fold calls.
Still open
  1. Where does the fusion-etv6-ntrk3 breakpoint fall relative to these boundaries, and is the junction codon actually mapped or only inferred from cDNA?
  2. Which of these parts are retained in the fusion, and is retention ever being confused with requirement for transformation?
  3. Do InterPro and the deposited crystal constructs agree with these UniProt boundaries? Where they do not, the disagreement should be recorded rather than silently resolved in UniProt's favour.
Every source behind this entry (1)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

    Human NTRK3 (NT-3 growth factor receptor) is 839 residues (UniProt Q16288) with the domain and region boundaries tabulated in this entry, and is referenced by 5 PDB entries.

    What this evidence cannot show

    Accession resolved by exact gene-name search restricted to reviewed human entries and confirmed against the gene symbol returned, because a previous lookup in this project silently resolved to the wrong gene. Coordinates are for the canonical isoform only; several of these proteins have isoforms that shift numbering. UniProt `Region` features are curator functional calls, not folds.

    Evidence that argues against this (1)
    • Domain boundaries are not a settled fact and differ between sources. InterPro, Pfam, SMART and individual crystal-structure constructs routinely disagree with UniProt by tens of residues, and published figures often use construct boundaries rather than database ones. Any downstream claim that a breakpoint falls just inside or just outside a domain is therefore only as firm as the boundary definition it assumes, which for every `Region` feature here is soft. InterPro Consortium 2026
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