Usage of InteR3M
InteR3M Homepage Homepage of InteR3M database provides a navigation bar (A), search bar (B) to search the database, brief introduction about the database and RNA Recognition Motif (RRM) domain, and allows users to filter the database with multicriteria search (C) according to their needs.
A) Navigation bar Navigation bar provides menu to navigate through the InteR3M database. Explore option allows users to explore Pfam families, RRM structural instances, ligand instance, and ligand structures. Help option provides help for InteR3M database. The About option provides the links to InteR3M data dictionary and some general information like statistics, release notes of InteR3M.
B) Search bar Search InteR3M with UniProtKB Name, UniProtKB Accession number, RRM Name, and/or PDB identifier. For example, RRM domains from "Protein sex-lethal" can be searched using UniProtKB Accession number P19339. Every search will return results with a list of matching RRM instances and/or RRM structures.
Along with the search, the InteR3M database can be filtered with one or more parameters for several outputs using multicriteria search. The multicriteria search allows users to search for contacts, structures, experiments, RRM sequences, and/or Ligand sequences. User have to enter a value in at least one of the field for the filters to work. User can enter values in multiple fields for each filter to retrieve very specific results. For example, to retrieve all hydrogen bonds from structure 1B7F, select Search Contacts, enter "1B7F" in PDB ID field, select "H-bond" from Interaction type field, and click on Search.
The search results provide a list of matching RRM domain instances and structures. The above image shows the search results for P19339. User can select any of the RRM or protein from results to get the detailed view.
InteR3M Data Dictionary
Data dictionary for InteR3M database is created using dbdocs. Explore the data dictionary here.
InteR3M Definitions
RRM Entrynames RRM Entryname is a unique identifier for RRM domain instances. e.g. P08579_RRM1. RRM Entryname consists of up to 15 alphanumeric characters with a naming convention that can be symbolized as X_Y, where
- X is UniProt accession number e.g. P08579
- The '_' sign serves as a separator;
- Y is the concatenation of RRM and sequential position of RRM domain instance in the corresponding protein.
RRM Structure ID RRM Structure ID or Name is a unique identifier generated for RRM structures, e.g. 1A9NB01. RRM Structure ID is built by concatenation of PDB identifier, chain identifier and the sequential position of RRM domain in the corresponding PDB chain.
Experiments in InteR3M InteR3M database considers two broad types of experiments (in fact all experiments in InteR3M are classified under one or the other of these two types).
Structural experiments: This type of experiment results in a 3-D structure of protein(s) with or without the interacting ligand. One PDB entry is considered as one Structural experiment. It might have one or more proteins with or without one or more ligands.
Non-structural experiments: This type of experiment does not result in a 3-D structure. The goal of these experiments is to check the binding of protein and ligand. An instance of "Non-structural experiment" is usually an experiment performed to check the binding of single ligand with one protein containing one or more RRM domains.