What is Genome Location Browser?
The genome browser is a hierarchical representation of structures from genomes of various organisms.
RCSB PDB has mapped the structures to the chromosomal loci based on UniProtKB/GenBank accession numbers associated with the structures and the loci. The genomes represented are a subset of the genomes in the NCBI genome database and whose curated sequences for genetic loci are archived at Entrez Gene. The top level in the hierarchy is the organism's genome. Each genome expands into chromosomes which in turn expand into a list of loci on the chromosomes. Each locus is a link to retrieve structures associated with it.
Why Browse by Genome Location?
Here you can search for an organism's name and browse through genes in the organism by Chromosomes or gene names. You can also search the mapped structures using their names.
How to use the Genome Location Browser?
This browser combines two different ways of organizing polymer entities - by organism and by position of the gene of interest in a chromosome.
- You can search for a specific gene by its name and find the first instance of it in any organism included in the browser.
- If you are looking for a gene in a specific organism you can first search for the organism by its name and then
- browse through all the chromosomes to find the gene of interest, OR
- find the chromosome number on which the gene of interest is located and browse the relevant chromosome. To find the chromosome number where the gene of interest is located you can search for the organism and gene name in the Entrez Gene website.
Once you have identified a gene of interest in the organism of your choice, you can view the number of associated polymer entities in the PDB, and select from them the ones to explore.
1. Search for TEM-1 Class A Broad Spectrum beta-lactamase protein in E. coli
- Type the name of the organism "Escherichia coli" or "(E. coli) " in the search box at the top of the page and click on search
- Scroll down the page to where the selected organism is highlighted in the browse tree - click on the arrowhead (triangle) next to the organism name to open the genes listed under it.
- The numbers listed next to the gene name (class A broad-spectrum beta-lactamase TEM-1) indicate the number of polymer entities that match the gene name. Clicking on it will launch a search for all polymer entities in the PDB that are associated with the organism and gene name.
2. Search for Cadherin 1 in Homo sapiens
- Type the name of the organism "Homo sapiens" in the search box at the top of the page and click on search
- Scroll down the page to where the selected organism is highlighted in the browse tree - click on the arrowhead (triangle) next to the organism name to open the chromosomes listed under it.
- To find out the chromosome that includes the gene of interest, do a quick check in the Entrez Gene website on a new browser window or tab. Open this page and type "Homo sapiens cadherin 1" in the top search box. Scan the page showing the results of the search and note the chromosome number (16) on which the gene is located.
- Come back RCSB page where you have the Genome Location Browser open and click on the arrowhead (triangle) next to the Chromosome 16 to view the genes listed under it. Note only genes whose proteins are present in the PDB are listed here.
- The numbers listed next to the gene name (Cadherin 1) indicate the number of polymer entities that match the gene name. Clicking on it will launch a search for all polymer entities in the PDB that are associated with the organism and gene name.