Proteinstrongking

KDM5A (JARID1A / RBP2 H3K4 demethylase) domain architecture

also called KDM5A · JARID1A / RBP2 H3K4 demethylase

KDM5A is the 3' partner of NUP98::KDM5A. 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 KDM5A (UniProt P29375, 1690 aa). An H3K4me3 demethylase. Three PHD fingers at 293-343, 1161-1218 and 1607-1661, and a JmjC catalytic domain at 437-603. Created so the 3D fusion viewer can resolve fusion-nup98-kdm5a, 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

Lysine-specific demethylase 5A1,690 aa

loading AF-P29375-F1…

AlphaFold AF-P29375-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-nup98-kdm5a: no protein entry for KDM5A. 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

Part	Residues	Kind	Precision
JmjN	19-60	Domain	firm
ARID	84-174	Domain	firm
JmjC	437-603	Domain	firm
PHD-type 1	293-343	Zinc finger	firm
C5HC2	676-728	Zinc finger	firm
PHD-type 2	1161-1218	Zinc finger	firm
PHD-type 3	1607-1661	Zinc finger	firm
Interaction with LMO2	1623-1690	Region	soft
GSGFP motif	419-423	Motif	soft

46 PDB entries reference this protein.

Facts and figures

uniprot	P29375
gene symbol	KDM5A
length AA	1690
protein name	Lysine-specific demethylase 5A
alphafold ID	AF-P29375-F1
n PDB total	46
uniprot verified	true
accession resolution	exact gene-name search, reviewed human only, gene symbol confirmed in the response
created for	fusion-nup98-kdm5a

domains

domains — the numbers behind the chart

[
  {
    "name": "JmjN",
    "start": 19,
    "end": 60,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "ARID",
    "start": 84,
    "end": 174,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "JmjC",
    "start": 437,
    "end": 603,
    "feature_type": "Domain",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "PHD-type 1",
    "start": 293,
    "end": 343,
    "feature_type": "Zinc finger",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "C5HC2",
    "start": 676,
    "end": 728,
    "feature_type": "Zinc finger",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "PHD-type 2",
    "start": 1161,
    "end": 1218,
    "feature_type": "Zinc finger",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "PHD-type 3",
    "start": 1607,
    "end": 1661,
    "feature_type": "Zinc finger",
    "note": "UniProt folded-domain call.",
    "boundary_precision": "firm"
  },
  {
    "name": "Interaction with LMO2",
    "start": 1623,
    "end": 1690,
    "feature_type": "Region",
    "note": "UniProt functional region, not a fold boundary. Soft edges; render as low confidence.",
    "boundary_precision": "soft"
  },
  {
    "name": "GSGFP motif",
    "start": 419,
    "end": 423,
    "feature_type": "Motif",
    "note": "UniProt functional region, not a fold boundary. Soft edges; render as low confidence.",
    "boundary_precision": "soft"
  }
]

PDB IDS

[
  "2JXJ",
  "2KGG",
  "2KGI",
  "3GL6",
  "5C11",
  "5CEH",
  "5E6H",
  "5ISL",
  "5IVB",
  "5IVC",
  "5IVE",
  "5IVF",
  "5IVJ",
  "5IVV",
  "5IVY",
  "5IW0",
  "5IWF",
  "5K4L",
  "5V9P",
  "5V9T",
  "6BGU",
  "6BGV",
  "6BGW",
  "6BGX"
]

How this could bite us back

Nothing here licenses targeting any part of KDM5A. 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

Where does the fusion-nup98-kdm5a breakpoint fall relative to these boundaries, and is the junction codon actually mapped or only inferred from cDNA?
Which of these parts are retained in the fusion, and is retention ever being confused with requirement for transformation?
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)

E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
Human KDM5A (Lysine-specific demethylase 5A) is 1690 residues (UniProt P29375) with the domain and region boundaries tabulated in this entry, and is referenced by 46 PDB entries.
UniProtKB P29375 (KDM5A_HUMAN): sequence length, domain, zinc-finger, DNA-binding, repeat, motif and region features, and PDB cross-references · UniProt Consortium · UniProtKB 2026
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

Connected to

part of →NUP98::KDM5A (NUP98-JARID1A), t(11;12)(p15;p13)
reference domain coordinates for the KDM5A side of this fusion
analogous to →NSD1 (nuclear receptor-binding SET domain protein 1) domain architecture
both are chromatin-modifying enzymes fused to the same 5' partner, NUP98, and both retain a reader module; a controlled comparison of what NUP98 contributes versus what the enzyme does