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Variants on protein structures part 6: BRAF V600 in the activation loop

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.

BRAF encodes a serine/threonine kinase of the MAPK pathway, which passes growth signals from RAS to MEK. In about half of melanomas, and in thyroid and colorectal tumours, one base change turns valine 600 into glutamate (V600E), and the kinase signals without RAS. Vemurafenib and dabrafenib inhibit the mutant kinase. We open the codon beside a crystal structure of the V600E kinase domain and read which of the kinase domain's conserved sites it falls in. We'll:

  • open BRAF in the protein browser with structure 4MNF, and pin the human row of the ortholog alignment
  • highlight and label codon 600 and read ClinVar's records at it
  • 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
The BRAF V600E kinase domain bound to GDC-0879, PDB 4MNF4MNF.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 BRAF on codon 600

Part 1 walks through the protein browser's linked session. Open it on BRAF with structure 4MNF:

  • open genomes.jbrowse.org/protein-browser/?gene=BRAF&ref=9606&structure=4mnf and click Open in JBrowse ↗
  • close the AlphaMissense track with the × on its label
  • type chr7:140753306-140753366[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
  • drag across the scale bar over codon 600 and pick Highlight region, then click the link chip at the top of the band, pick Edit label... and type V600

The link names no residue. With residue=600 in it, the protein browser opens the seed alignment of the kinase domain's Pfam family, kinases of many genes and species, in place of BRAF's orthologs.

Hover codon 600 on the gene. The protein view's header compares the two letters: valine in the genome, glutamate in the crystal. 4MNF leaves most of the activation loop past residue 600 unmodelled, so the cartoon breaks off there.

BRAF at codon 600 with ClinVar, the ortholog alignment pinned to its human row, and the 4MNF kinase domain dimer. The hovered codon, the alignment column and Glu600 mark one position. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Every row of the alignment has valine at 600. ClinVar stacks records of several base changes on the codon; 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
  • in the protein view's palette menu, pick Domains from the alignment
BRAF in three linked views, colored by the alignment's domains and sites: the genome's domain track, the alignment's rows and the 4MNF cartoon, with each site's side chains as sticks. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Codon 600 sits inside the activation loop, one of NCBI's sites of the STKc_Raf kinase domain. The ATP binding site ends upstream, at Asp594 of the DFG motif.

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 3OG7, BRAF V600E bound to vemurafenib, whose first chain leaves residue 600 unmodelled

See also

Citations