SGD Help: PDB Homologs

Contents

• Description
• Organization of the results page
• Relevant Links
• Relevant Glossary Terms

Description

This page presents information for the proteins of known structure with sequence similarity to the specified Saccharomyces cerevisiae protein. The results will display both the yeast protein structure (if it has been solved) and other proteins of known structure, regardless of source, that have sequence similarity to the query protein.The analysis was performed by comparing yeast protein sequences against protein sequences in The RCSB Protein Databank (PDB) using the Smith-Waterman analysis program. All hits with E-value less than or equal to 0.01 are displayed.

Organization of the results page

1. Locus Info page gives detailed information about the gene ACT1, including information about its ORF, literature published on this gene name, GO annotations for ACT1 and more.
   
2. Protein Motifs takes you to the results page for the protein motifs found in the query protein against motifs in the eMOTIFS database.

Details of the Results Table

• Column 1: Titled PDB protein structure(s) homologous to ACT1 has two sub columns.
  • The first of these lists the names of the PDB homologs (like 1yag) followed by the peptide chain name ( Chain:A) (if relevant) and then the name of the structure (Structure of the yeast actin-human gelsolin segment 1 complex). Sometimes a proteins exists as multimers and the crystal structure of the mulitmer is determined. In such cases, each peptide chain in the multimer is denoted by a chain name like Chain: V, W, X, Y, Z as shown below.
  • The second of the subcolumns provides links to the associated PDB information page, the PDB structure page where you can visualize the 3-dimensional structure of the homolog protein in an interactive fashion and a reference associated with the structure of the homolog as given by PDB.
• Column 2: Titled Homolog Source (per PDB) lists the source of the crystallized homolog protein (1yag in this case). This information is retrieved from the PDB.
• Column 3: Titled Protein Alignment: ACT1 vs Homolog has 4 subcolumns within.
  • The first of these titled P-Value refers to the probability of obtaining, by chance, a pairwise sequence comparison of the observed similarity given the length of the query sequence and size of the database searched. Thus, low P-values indicate sequence similarities of high significance.
  • The second of these titled %Identical indicates the % of amino acid residues that are identical between the query protein (ACT1 here) and the homolog.
  • The third of these titled %Similar indicates the % of amino acid residues that are similar between the query protein and the homolog. The number indicated by %Similar excludes the number that are identical.
  • The fourth of these titled Alignment provides a link to view the sequence alignment of the query protein and the homolog.
• Column 4: Titled External Links provides links to other protein structure databases like SCOP-Structural Classification of Proteins , MMDB-Molecular Modelling Database maintained by NCBI and CATH-Class, Architecture, Topology and Homologous superfamily. For more information on any of these sites, you are better served at the original source.

  16 PDB homolog(s) found for yeast gene ACT1/YFL039C	ACT1/YFL039C links Locus Info Protein Motifs

  PDB protein structure(s) homologous to ACT1		Homolog Source (per PDB)	Protein Alignment: ACT1 vs. Homolog				External Links
  			P-Value	%Identical	%Similar	Alignment
  1yag ( Chain: A) Structure of the yeast actin-human gelsolin segment 1 complex	PDB_Info PDB_Structure	Saccharomyces cerevisiae | Homo sapiens	7.5e-261	100	0	View alignment	SCOP MMDB CATH
  1alm ( Chain: V, W, X, Y, Z) The structure of the acto-myosin subfragment-one complex. results of searches using data from electron microscopy and x-ray crystallography. theoretical model, alpha carbons.	PDB_Info PDB_Structure Reference	Gallus gallus | Oryctolagus cuniculus	Chain V = 5.2e-231	87	7	View alignment	SCOP MMDB CATH
  			Chain W = 5.2e-231	87	7	View alignment
  			Chain X = 5.2e-231	87	7	View alignment
  			Chain Y = 5.2e-231	87	7	View alignment
  			Chain Z = 5.2e-231	87	7	View alignment

  Relevant Links

  • The RCSB Protein Databank (PDB)
  • eMOTIFS database
  • SCOP-Structural Classification of Proteins.
  • MMDB-Molecular Modelling Database maintained by NCBI.
  • CATH-Class, Architecture, Topology and Homologous superfamily.
  • Help for PDB Homologs Query page
  • Protein Viewer Resource page

  Relevant Glossary Terms:

  • Alignment
  • Smith-Waterman alignment
  • ORF-name
  • P-value
  • PDB
  • Query Sequence

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