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Variants on protein structures part 3: seedless grapes on an AlphaFold model

JBrowse v5 beta

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Most seedless grapes owe it to one missense change in VviAGL11, a MADS box transcription factor that regulates seed development. Arginine 197 becomes leucine (R197L), and among the cultivars tested only this change was fully linked with seedlessness (Royo et al. 2018). The PDB has no structure of the protein, so we open the codon beside its AlphaFold model and read how confident the prediction is at residue 197. We'll:

  • open VviAGL11 on codon 197 from the protein browser, on the Pinot Noir reference
  • hover the codon's alignment column to find its residue on the model
  • read the model's confidence colors around residue 197 and in the MADS domain

The model is of UniProt A0A217EJJ0, a protein sequenced from the seedless cultivar Sultanina (Thompson Seedless), so residue 197 of the model is leucine, where the Pinot Noir genome codes arginine.

Prerequisites

  • for your own JBrowse, the protein3d and msaview plugins from the plugin store; genomes.jbrowse.org already loads them

The data

Nothing to download: the protein browser and the plugins read these files by URL. Your own model opens a model of your own.

The files
What it isFile
The Pinot Noir 40024 reference and its NCBI RefSeq genes, through UCSC's GenArk hub GCF_030704535.1GCF_030704535.1/
The AlphaFold model of A0A217EJJ0, with its per-residue confidenceA0A217EJJ0
UniRef, the rows of the alignmentuniref

Opening VviAGL11 on codon 197

NCBI names the gene MADS5 (NM_001281189.1), on the minus strand of chr18. Open the protein browser on residue 197:

  • open genomes.jbrowse.org/protein-browser/?gene=AGL11&ref=29760&residue=197 and click Open in JBrowse ↗
  • type chr18:32255673-32255763[rev] into the location box. [rev] keeps the minus-strand gene reading left to right
  • click Reset Zoom, the circular arrow at the top right of the structure, to fit the whole model
  • hover column 197 of the wine_grape_query row in the alignment

The structure opens colored by pLDDT, AlphaFold's per-residue confidence, which the palette icon in the protein view's header sets for any model under pLDDT confidence (AlphaFold). Dark blue is very high, light blue confident, yellow low and orange very low, and the header's pLDDT row draws the same scale along the sequence.

VviAGL11 at codon 197 with its UniRef alignment and the AlphaFold model colored by pLDDT. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Arginine fills most rows of the alignment column, muscadine grape's included. Residue 197 falls in AlphaFold's low band, where AlphaFold DB advises treating the chain's placement with caution, and the DNA-binding MADS domain falls in the very high band.

Your own model

The protein view takes a model of your own as well:

  • Launch protein view in a gene's right-click menu, then its File or URL tab, opens a PDB or mmCIF of your own, such as a ColabFold or AlphaFold 3 model
  • the protein browser's chips open other organisms on a residue each, on genomes.jbrowse.org's GenArk assemblies

See also

Citations

  • Royo C, Torres-Pérez R, Mauri N, et al. The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11. Plant Physiol 2018;177:1234-1253. https://doi.org/10.1104/pp.18.00259
  • Varadi M, Bertoni D, Magana P, et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res 2024. https://doi.org/10.1093/nar/gkad1011