NCBI Tutorial Notes BSCI 410 Spring 07/Liu1Ch 5: Structure (Click on Structure at the top black bar of the NCBI homepage)Structural databases such as Entrez Structure at NCBI contain details of proteinstructure based on X-ray crystallographic and NMR studies. From this database it ispossible to retrieve and examine a particular three-dimensional structure in a viewercalled Cn3D. In this tutorial, we will examine some structures and learn to use theCn3D structural viewer.Download Cn3D v4.1 by clicking on Cn3D v4.1 on the left-hand side menu.Type 1JM6 (the ID for rat pyruvate dehydrogenase in the PDB proteindatabase)-Click Go.When the result appears, click 1JM6 to see the NCBI Molecular ModelingDatabase (MMDB) Structure Summary pageClick "View 3D Structure"You will see alpha helices are shown as green cylinders and beta pleated sheetsas gold flat arrows. The connecting amino acid chain is in blue.Use your mouse to drag the molecule and rotate it. Note that it consists of twomirror image complexes consisting of the A and B chains. Notice the bound ADPmolecule in each complex (partly colored in red and complexed with a Mg ion)? Can youidentify the adenine ring structure in the ADP molecule? You can zoom in using theZoom feature under View in top menu.The lower pop-up window (Sequence/Alignment Viewer) shows the primarysequence of the two amino acid chains. Note that the sequence is color coded to matchthe 3D structure.On the top menu, try style such as frame and spacefillGo back to Structure by clicking Structure on the very topDo another search with GCN4 and yeast-Go, you will get a list (4 pages)Click on 1YSA (on page 4)Click View 3D-you will see both protein chains interacting with DNAGo back to Structure[Click VAST (Vector Alignment Serach Tool)VAST allows an investigator to search the database for structures similar to theone of interest. This allows a crystallographer with a newly acquired sequence to searchfor structurally related proteins utilizing the VAST program.Search for 1G5S, then try click domain 2, click VAST]-optionalCh 6: OMIM (Online Mendelian Inheritance in Man)Click on statistics on the left (under OMIM facts)A Table shows all the genes entered in OMIM (about half of the 35,000 humangenes are shown)Click on X-linkedClick on the first entry-get the description about the geneGo back to OMIM, Click on Update Log (just below Statistics)See the record is updated every monthGo back to OMIM, enter "Huntington" in the search window-GoYou will get 107 entriesClick on the the first entry (OMIM number *143100)See the wealth of info on this diseaseClick on Map "4p16.3" -get a table- click 4p16.3 in the top of tableNCBI Tutorial Notes BSCI 410 Spring 07/Liu2By zooming in on the locus (use the zoom in feature just above thechromosome graphic on the very left), we can display the genes that are locatedclose to the Huntington locus. Under the Morbid column are various loci associatedwith disease phenotypes.Click on HD under the "symb" columnLed to Entrez Gene record for the Huntington disease gene with linksto many information resourcesClick HGMD (the human genetic diseases database) on the right under LINK.HGMD is specializing in the nature of characterized mutations for various loci.Note the trinucleotide repeat for HDGo back to Entrez Gene,Scroll down, see the Genomic context, click "see HD in Mapview"Click "sv" (sequence view)-get to detailed molecular info on HDCh 7: Cancer Genome Anatomy Project (NCI-CGAP)Click on NCI-CGAP under Hot Spot on the NCBI Home pageClick on Cancer Genome Anatomy ProjectClick "Gene"Click "Gene Finder" (third in the list)Enter "BRCA1" (Breast Cancer Associated1) and Submit queryClick "Gene Info"Under Database Links, Click UniGene (UniGene entry is a set oftranscript sequences that appear to come from the same transcription locus)together with information on protein similarities, gene expression, cDNA clonereagents, and genomic location.Click "Entrez Gene", exploreClick "OMIM", exploreGet back to CGAP by clicking to panelClick "Pathway"Click on the BioCarta PathwaysClick on "ATM Signaling Pathway"The ATM pathway is important for delaying cell cycle progression toallow time for repair if there has been damage to DNA. This helps to preventpermanent damage or chromosome breakage and the consequent genomicinstability. Maps of this type help the researcher place a particular geneproduct into a broader context. BRCA1 is shown just to the left of center.Clicking on any of the icons in the map will takes us back to the GeneInfo page for that geneGet back to CGAP-Click "genes" againClick on the Gene Ontology (GO) browserGO defines function in a hierarchical fashionClick "+" sign next to the three terms in turn to open up the nextlevel of the hierarchyClick + next to Molecular FunctionClicking + sign next to 'binding' and then 'nucleic acid binding'Click on the number to see the list of genes belonging to thatcategoryGet back to CGAP-click "chromosomes"Click on FISH-mapped BACs, click on chromosome 1Click on Physical SNP map, click on chromosome
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