SGD Help: PDB Homologs

The PDB Homolog Query page allows searches for structural information on proteins of known structure with sequence similarity to the specified Saccharomyces cerevisiae protein. The search will retrieve the "PDB Homolog" page for that yeast protein, if it is available. The PDB Homolog page will list the yeast protein structure (if it has been solved) along with other proteins of known structure, regardless of source, that have sequence similarity to the query protein. The PDB Homolog page also provides further links to structural and alignment information for these proteins. The analysis was performed by comparing yeast protein sequences against protein sequences in the RCSB Protein Data Bank (PDB) using WU-BLAST.

Contents

1. PDB Homolog Query
   1. Using the PDB Homolog Query Page
   2. Accessing the PDB Homolog Query Page
2. PDB Homolog Results
   1. Organization of the Results Page
   2. Details of the Results Table
3. Protein Alignments
   1. Alignment Details
   2. Alignment Position
   3. Sequence Alignment
   4. Homolog Structure

PDB Homolog Query

Using the PDB Homolog Query Page

There are four different Query Options, listed below. Ultimately, each option will retrieve a PDB Homolog page for a Saccharomyces cerevisiae protein, if that information is available. The options vary in that some have intermediate "retrieved lists" where you can choose among yeast proteins that have PDB Homologs and also meet the specified parameters.

Gene/ORF Name: Enter a Saccharomyces cerevisiae gene or ORF to retrieve a list of PDB Homolog page for the query yeast gene or ORF name, along with links to structural and alignment information.

Keyword: Enter a text keyword to retrieve a list of yeast genes, along with their respective PDB Homologs, where the keyword has a match in the "Gene Product" field or "GO annotations" in SGD. The retrieved list provides further links to the PDB Homolog pages.

PDB Identifier: Enter a PDB Identifier to retrieve a list of yeast proteins with sequence similarity to a protein listed in PDB. The retrieved list provides further links to the PDB Homolog pages.

Chromosome: Choosing a Chromosome number retrieves a list of all genes on that yeast chromosome that have either solved protein structures or sequence similarity to proteins with solved structures. The retrieved list provides further links to the PDB homolog pages.

Accessing the PDB Homolog Query Page

The PDB Homolog Query page can be accessed by selecting the "PDB Search" link from the Homology section of the Sequence pull-down menu of the SGD toolbar. Selecting the PBD Homologs link from any SGD locus page retrieves a PDB Homolog page for that gene, if it is available, along with links to structural and alignment information.

PDB Homolog Results

Organization of the Results Page

This page displays the retrieved PDB homologs for the yeast query protein. Organization of the results page is described below with ACT1 as an example yeast query protein (only part of the results table is shown below to highlight the main features).

Title of the table 127 PDB homolog(s) found for yeast gene ACT1/YFL039C tells you the total number of homologs found in PDB for the query protein (ACT1 in this example).

Details of the Results Table

The query results are presented in a table with four columns: PDB protein structure(s) homologous to ACT1, Homolog Source (per PDB), Protein Alignment: ACT1 vs. Homolog, and External Links.

• PDB protein structure(s) homologous to ACT1 - Presented in two subcolumns.
  • 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: C, I, A, G, M, L, E, N, K, J, H, B, D, F 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.
• Homolog Source (per PDB) - Lists the source of the crystallized homolog protein (1YAG in this case). This information is retrieved from the PDB.
• Protein Alignment: ACT1 vs Homolog - Presented in four subcolumns.
  • The first of these lists the P-Value, indicating 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 lists %Identical, indicating the % of amino acid residues that are identical between the query protein (ACT1 in this example) and the identified homolog.
  • The third of these lists %Similar, indicating the % of amino acid residues that are similar between the query protein and the identified homolog. The number indicated by %Similar excludes the number that are identical.
  • The fourth of these provides a link to the sequence Alignment of the query protein and the identified homolog.
• External Links - Provides links to other protein structure databases like SCOP-Structural Classification of Proteins, MMDB-Molecular Modelling Database maintained by NCBI, and CATH Protein Structure Classification. For more information on any of these sites, please go to the original source.

Protein Alignments

The Protein Alignment page compares a protein of known structure to your Saccharomyces cerevisiae query protein. The analyses are performed by comparing yeast protein sequences against protein sequences in The RCSB Protein Databank (PDB) using WU-BLAST. The PDB homolog is labeled with the unique identifier assigned by PDB. Near the top of the page (located directly above the "Alignment Details" section), clicking on the PDB ID or on the "Jump to Structure" button will skip to the protein structure and a brief description of the PDB homolog located at the bottom of the page. The PDB homolog may be from any species, including S. cerevisiae.

Alignment Details

This section displays the following statistics which describe the extent of similarity between the S. cerevisiae protein and the PDB Homolog:

Protein Length: Predicted length of the S. cerevisiae protein, in amino acids.

Alignment Length: Number amino acids included in alignment and, in parantheses, the percentage of the S. cerevisiae protein with which the PDB Homolog aligns.

P-value: An indication of the significance of the sequence similarity (lower is better).

%Identity: Percentage of amino acids in the alignment which are identical between species. In both the "Alignment Details" section and in the "Sequence Alignment" section, %Identity is labeled in yellow.

%Similarity: Percentage of amino acids in the alignment which are not identical between species, but which have similar biochemical properties and are considered interchangeable in many situations. In both the "Alignment Details" section and in the "Sequence Alignment" section, %Similarity is labeled in light green.

Alignment Position

This section provides a graphic display of the alignment between the two proteins. The number bar at the top of the display indicates the amino acids position in the S. cerevisiae protein. The blue (top) bar represents the S. cerevisiae protein and the red (bottom) bar reprents the PDB homolog. The relative position of the red bar indicates the portion of the S. cerevisiae protein to which the PDB homolog aligns. In this example, the Alignment Position Display shows that the PDB homolog, 1i84_S aligns with amino acids 374-519 of the S. cerevisae protein, Cog8p.

Sequence Alignment

This section displays the sequence alignment between the two proteins. The top line is the S. cerevisiae protein sequence, the bottom line is the PDB homolog sequence. Amino acids that are identical between proteins are labeled in yellow. Amino acids that are similar between proteins are labeled in light green.

In this section, clicking on the S. cerevisiae gene name will open a new window showing the SGD Locus Summary page for that gene, while clicking on the PDB ID will open a new window containing the PDB summary information for that protein at The RCSB Protein Databank (PDB).

Homolog Structure

This section displays information about the PDB homolog, as provided by The RCSB Protein Databank (PDB).

The left side of this section contains the following details and links for this protein structure:

PDB Protein Identification: PDB ID, followed by a brief description of the PDB homolog.

PDB Info: link to the PDB summary information for this protein structure.

Homolog Source: Organism in which this protein in encoded.

External Links: Links to other databases which may contain information about this protein structure, including Structural Classification of Proteins (SCOP), NCBI's Molecular Modeling DataBase (MMDB), and the Class, Architecture, Topology and Homologous superfamily (CATH) protein structure classification.

The right side of this section displays a ribbon diagram of the structure. Clicking on the ribbon diagram will open a new window at The RCSB Protein Databank (PDB) containing the PDB summary information for this protein structure.

Go to PDB Homolog Query