TP53 from prediction to crystal
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The p53 protein has a predicted structure covering every residue and crystal structures covering the parts that fold. We open three of them in one view beside the TP53 gene, each mapped to the same transcript, click a cancer hotspot on a crystal to find its codon, and open an NMR ensemble of the transactivation domain. The protein3d plugin maps each structure to the transcript, and Mol* draws the structures.
Prerequisites
- the protein3d plugin. In your own JBrowse, install it from the plugin store; the hosted config the links open already loads it
Where the data comes from
Nothing to download: the links open a hosted hg38 config with NCBI RefSeq genes, and the protein3d plugin fetches these files when a link opens.
The files
- the AlphaFold model of p53, UniProt P04637: https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.cif
- the p53 core domain bound to DNA, PDB 1TUP: https://files.rcsb.org/download/1TUP.cif
- the p53 transactivation peptide bound to MDM2, PDB 1YCR: https://files.rcsb.org/download/1YCR.cif
- the p53 transactivation domain bound to CBP, solved by NMR, PDB 2L14: https://files.rcsb.org/download/2L14.cif
- UniProt's feature annotation of p53, the domain and variant tracks: https://rest.uniprot.org/uniprotkb/P04637.gff
- SIFTS, which maps where each crystal's residues sit in the UniProt sequence: https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/1tup
Opening three TP53 structures mapped to one transcript
An AlphaFold model is one chain, numbered like the UniProt sequence. A crystal structure often holds one domain of the protein, numbered from wherever the crystallised construct began. The plugin maps both kinds to the gene by aligning the structure's sequence to the transcript's translation.
Open the three structures of TP53. The plugin superposes the structures with TM-align, and the Color menu is set to Mapped chain, which colors the chain the transcript encodes blue and everything else grey.
The arrow beside each structure in the header opens its alignment panel, with the transcript's translation on the GENOME row, the structure's sequence on the STRUCT row and a ruler in the authors' residue numbering:
- AlphaFold is one unbroken match. Under its STRUCT row, pLDDT (AlphaFold's per-residue confidence) is high across the core and falls away at both ends, the same tails both crystals leave out.
- 1TUP covers the DNA-binding core alone, and its ruler starts at 94, the residue where the crystallised construct begins.
UniProt annotations on the 1TUP core-domain crystal
The feature tracks under each panel come from UniProt, shifted to the construct's numbering with the SIFTS offset. Show all feature tracks in the display settings menu adds secondary structure, modified residues and other minor types to the default domains, binding sites and variants.
1TUP holds three copies of the core and two DNA strands. The panel's Mapped chain picker lists them, and the plugin chose the protein entity because its sequence aligns to the transcript. Hovering any copy in the 3D canvas highlights the same residue on the genome.
Finding the codon of the R248 hotspot from the crystal
Open the 1TUP panel and click the R248 hotspot on its STRUCT row, or open the same session with R248 selected. The ruler and the transcript row give the same number, because the 1TUP authors numbered their construct the way UniProt numbers the whole protein.
Hovering the codon on the gene highlights the residue on the structures that contain it; hovering the intron beside the exon highlights nothing.
Choosing the mapped chain in the MDM2 complex 1YCR
1YCR holds the N-terminal domain of MDM2, a p53 regulator, and a fifteen-residue peptide from the p53 transactivation region, and the transcript encodes the peptide. Open the 1YCR panel: its Mapped chain picker lists both chains, and the plugin picked the peptide, a short exact match near the start of the transcript row.
Switch the picker to Chain A. The plugin realigns against MDM2, which turns blue, and the GENOME row becomes a scatter of gapped fragments, because the transcript does not encode MDM2.
The p53 transactivation domain as an NMR ensemble
PDB 2L14 holds residues 13 to 61 of the p53 transactivation domain, the region where the AlphaFold pLDDT falls away, bound to the nuclear coactivator binding domain of CBP. Its authors deposited an NMR ensemble of twenty models that each fit the data.
Open 2L14 with its two helices selected.
The link selects the two helices the file annotates, residues 18 to 26 and 46 to
54, through initialTranscriptResidues, which counts along the transcript's
translation. The view opens slowly because the plugin loads each model as a
separate structure. Click Reset Zoom, the circular arrow at the top right of
the canvas, to fit the whole ensemble.
The grey spray on the right is the C-terminal tail of CBP. The first helix lies within the stretch the 1YCR peptide covers, and its codons straddle an intron, so its band on the gene splits across two exons.
Checking the R248 codon against the reference sequence
In the R248 session's genome view, zoom into the band the selection drew on
TP53, down to base level, and tick Reference sequence in the track
selector. The transcript is on the minus strand, so the codon under the band
reads CCG left to right on the reference track, which is CGG, arginine, on
the transcript.
Structures of your own gene
The protein3d plugin is in the plugin store: install Protein3d from the Tools menu, then right-click a gene and choose Launch protein view to open its AlphaFold model. For several structures at once, write the view as a session spec. This is the spec behind the three-structure link. Swap the UniProt accession, the PDB ids, the transcript and the locus for your gene's, and name a gene track your config has:
{
"views": [
{
"type": "ProteinView",
"structures": [
{ "uniprotId": "P04637" },
{ "pdbId": "1TUP" },
{ "pdbId": "1YCR" }
],
"transcriptId": "NM_000546.6",
"colorScheme": "mapped-chain",
"connectedView": {
"assembly": "hg38",
"loc": "chr17:7,671,000-7,684,500",
"tracks": ["hg38-ncbiRefSeq"]
}
}
]
}Try this example live ↗ · Open it in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)
The transcript has to be in one of the connectedView tracks at loc, since
the plugin maps each structure by aligning its sequence to that transcript's
translation.
See also
- Tutorial: Proteins on genomes.jbrowse.org
- Docs: URL query parameter API
External links
Citations
- Cho Y, Gorina S, Jeffrey PD, Pavletich NP. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 1994.
- Kussie PH, Gorina S, Marechal V, et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 1996.
- Lee CW, Martinez-Yamout MA, Dyson HJ, Wright PE. Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein. Biochemistry 2010.
Feedback on this tutorial is welcome: contact us.