A Specificity Map for the PDZ Domain Family
This data is supplementary material for:
A Specificity Map for the PDZ Domain Family
Raffi Tonikian1,2,9, Yingnan Zhang3,9, Stephen L. Sazinsky4, Bridget Currell5, Jung-Hua Yeh6, Boris Reva7, Heike A. Held3, Brent A. Appleton3, Marie Evangelista5, Yan Wu8, Xiaofeng Xin1,2, Andrew C. Chan6, Somasekar Seshagiri5, Laurence A. Lasky3, Chris Sander7, Charles Boone1,2, Gary D. Bader1,2,7+, Sachdev S. Sidhu3+
1 Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada,
2 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
3 Department of Protein Engineering, Genentech, South San Francisco, California, United States of America
4 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
5 Department of Molecular Biology, Genentech, South San Francisco, California, United States of America
6 Department of Immunology, Genentech South San Francisco, California, United States of America
7 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
8 Department of Antibody Engineering, Genentech, South San Francisco, California, United States of America
9 These authors contributed equally to this work
+ Current Address: Terrence Donnelly Center for Cellular and Biomolecular Research and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
PDZ Data
This data has been submitted to the DOMINO (MINT) and PDZBase databases.
Please note the following corrections in the domain names in the HumanPDZ data set above:
- MAGI1-2 should be MAGI1-3
- MAGI1-4 should be MAGI1-5
- MAGI3-3 should be MAGI3-4
- MAGI3-2 should be MAGI3-3
File Format
Each zip file contains a set of peptide files as shown in the example below. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique. These files can be directly loaded into the LOLA software, which can be used to visualize peptide sets as sequence logos and to create Logo Trees, or the BRAIN software, which is a Cytoscape plugin that can be used to search protein sequence databases for proteins that contain sequence patterns matching a set of peptides.
The peptide file consists of a Header Section that describes the protein and domain sequence, and a Peptide Section that lists and describes the peptide ligands.
Example:
Gene Name DLG1 Accession Refseq:NP_004078 Organism Homo Sapiens (Human) NCBITaxonomyID 9606 Domain Number 3 Domain Type PDZ Interpro ID IPR001478 Technique Phage Display High Valency Domain sequence KVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVA Domain Range 466-525 Comment PeptideName Peptide CloneFrequency QuantData ExternalIdentifier 1 XLHFWRESSV 66 2 XXRLWKQTSL 3 3 ILKIWRETSL 3 4 KRTIWRETSL 2 A KNLRSNSMLG 2 6 HLKFWRSTRV 2 7 AHSKWRSTSV 2 8 XXXHRRETTV 1 9 VISRWRQTSL 1 10 TTWLGRQTRV 1 11 SRSSYRETSV 1 12 XXXSRRETSV 1 13 RLFRYRETSL 1 B PIRKRWTMTL 1 15 XXXNHRETSV 1 16 KIVRWKNTSV 1 17 KHRTWYETSV 1 18 XXXXFKQTSV 1 19 ARPKWRTTRV 1 20 ALPRRRETSV 1
Header Section
Describes the protein, domain, and experiment. Required fields are indicated with a *.
NOTE: This section is in a 2 column format. Field names must be separated from their values with a single TAB character. Multiple TABs, or spaces, are not accepted.
Gene Name:* An identifier that represents the gene or protein sequence. Not required to be unique.
Accession:* A space-separated list of database accession identifiers for the protein or corresponding gene.
Organism: Description of taxon of the protein.
NCBITaxonomyID*: Taxon identifier from NCBI's Taxonomy repository.
Domain Number*: A number that represents the position of the domain sequence within the protein. For proteins containing multiple instances of the domain, this number helps distinguish the position of these instances. Set to "0" if instance information is not known.
Domain Type:* The formal name of the domain, e.g. WW, PDZ, SH3.
Interpro ID: The Interpro database identifier for the domain.
Technique: The experimental method used to identify potential ligands of the protein.
Domain Sequence:* The amino-acid sequence of the domain region.
Domain Range: The amino-acid position range for the domain region within the protein.
Comment: Notes, additional information, personal comments pertaining to this file.
Peptide Section
Describes the experimentally determined peptide ligands. The peptide sequences must be in multiple alignment format. The sequences should contain no gaps, and should be padded with the X symbol on both sides, where required, such that all sequences have identical length.
NOTE: This section is in a 5-column format. Column headers and values must be separated with a single TAB character. Multiple TABs or spaces are not accepted.
Required fields are indicated with a *.
PeptideName:* A unique numerical symbol assigned to each peptide ligand. To omit a peptide, set to a non-numeric value (e.g. "A"). Values in this column must be unique.
Peptide:* The peptide ligand sequence.
CloneFrequency: Applies only to phage display data: the observed frequency of the peptide in the cloning step.
QuantData: A number that relatively or absolutely quantifies the protein-ligand interaction. E.g. The optical density (OD) from a protein chip experiment.
ExternalIdentifier: A database identifier for the peptide.
Supplementary Tables
Table S1 - Summary of analyzed C. elegans PDZ domains
Table S2 - Summary of analyzed human PDZ domains
Table S3 - SP values for human and C. elegans PDZ domains
Table S4 - PDZ domain specificity prediction
Table S5 - Prioritized endogenous and viral ligands for human PDZ domains
Table S6 - Prioritized endogenous ligands for the PDZ domains of DLG1
Table S7 - Known ligands for the PDZ domains of DLG1