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Variants on protein structures part 4: KRAS G12 in the GTP pocket

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.16. Desktop beta builds are coming soon.

KRAS encodes a small G protein that switches growth signalling on while it holds GTP. In tumours its missense mutations pile up on a few codons: glycine 12, glycine 13 and glutamine 61. A change at any of them keeps the protein in its GTP-bound, active state. The drug sotorasib binds KRAS G12C covalently at the mutant cysteine. We open the codon beside the crystal structure of that complex and read which of the protein's conserved sites the hotspots fall in. We'll:

  • open KRAS on codon 12 in the protein browser, with structure 6OIM, and pin the human row of the ortholog alignment
  • highlight and label codons 12, 13 and 61 on the genome
  • read ClinVar's records at the codon
  • color the genome, the alignment and the structure by the alignment's protein domains and sites

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, the plugins and the hosted hg38 config read these files by URL.

The files
What it isFile
KRAS G12C bound to sotorasib (AMG 510), PDB 6OIM6OIM.cif
ClinVar, which UCSC distributes as its ClinVar Variants track and the hosted hg38 config loadsclinvarMain.bb
NCBI's ortholog report, the rows of the alignmentrest-api/

Opening KRAS on codon 12

Part 1 walks through the protein browser's linked session. Open it on KRAS residue 12 with structure 6OIM:

  • open genomes.jbrowse.org/protein-browser/?gene=KRAS&ref=9606&residue=12&structure=6oim and click Open in JBrowse ↗
  • close the AlphaMissense track with the × on its label
  • type chr12:25245320-25245380[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
  • pick Use as reference row on the human_query tip of the alignment's tree, so a residue matching human draws as a dot

To label the hotspots, drag across the scale bar over codon 12 and pick Highlight region, then do the same for codon 13. Click the link chip at the top of each band, pick Edit label... and type G12 or G13.

Hover codon 12 on the gene. The hover lights the codon, the alignment column and the residue on the structure, and the protein view's header compares the two letters: glycine in the genome, cysteine in the crystal.

KRAS at codons 12 and 13 with ClinVar, the ortholog alignment pinned to its human row, and 6OIM. The hovered codon, the alignment column and Cys12 mark one position. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Every row of the alignment has glycine at 12 and 13. The other columns in the window are columns of dots too, so across these vertebrate orthologs the start of KRAS barely varies.

ClinVar has records of several base changes at each of codons 12 and 13. Click a box to open its record, which names the protein change, its classification and the conditions submitters reported.

The domains across all three views

The alignment view fills its rows with NCBI's conserved domains and sites, and the genome view and the structure read them from the alignment:

  • in the alignment view's menu, click Show domains on the genome, which adds a domain track to the genome view
  • in the genome view's menu, untick Show... → CDS reading frame colors
  • type chr12:25245328-25245372[rev] chr12:25227320-25227364[rev] into the location box, which puts codon 61, in the next exon, beside codons 12 and 13, and highlight it as Q61
  • in the protein view's palette menu, pick Domains from the alignment
KRAS in three linked views, colored by the alignment's domains and sites: the genome's domain track, the alignment's rows and the 6OIM cartoon, with each site's side chains as sticks. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Codon 12 sits inside three of NCBI's sites, the G1 box (the P-loop), the GTP/Mg2+ binding site and the putative GDI interaction site, and codon 13 inside the first two. Codon 61 sits in the Switch II region. The protein view's From the alignment rows list the same sites along the sequence, one row each, with the hovered residue as a vertical line.

Part 1 found the opposite at HBB codon 7: the sickle position lies outside the globin domain and every site, and the orthologs vary there.

Your own gene

  • any gene the protein browser opens takes the same steps, and a residue in the link opens the structure focused on it
  • Launch protein view in a gene's right-click menu picks another structure, such as 4OBE, KRAS bound to GDP with glycine at 12
  • the highlight list's menu imports a BED file, so a list of hotspot codons highlights in one step

See also

Citations