SRPDB

SRPDB (Signal Recognition Particle Database) is a specialized database dedicated to signal recognition particles (SRP), providing comprehensive information about the structure and function of these essential ribonucleoprotein complexes involved in protein translocation.

Overview

Signal recognition particles are universally conserved ribonucleoprotein complexes that play a crucial role in targeting nascent proteins to cellular membranes. SRPDB assists researchers in studying SRP by providing carefully curated, aligned, and phylogenetically organized sequences of both SRP RNA and protein components.

Database Contents

SRP RNA Sequences

SRPDB contains a total of 1,109 SRP RNA sequences organized into seven major phylogenetic groups:

• Short Bacterial (4.5S): 537 sequences
• Long Bacterial (6S): 96 sequences
• Archaeal: 81 sequences
• Protozoan: 82 sequences
• Fungal/Metazoan-group: 80 sequences
• Plant: 114 sequences
• Animal: 119 sequences

SRP Proteins

The database includes aligned and annotated sequences for all major SRP protein components:

• Core SRP Proteins: SRP9, SRP14, SRP19, SRP21, SRP54, SRP68, SRP72
• Chloroplast SRP: cpSRP43
• SRP Receptors: Alpha subunit (FtsY), Beta subunit
• Related Proteins: Flhf, CaM kinase II

Key Features

Multiple Sequence Alignments

All sequences are carefully aligned and can be browsed both phylogenetically and alphabetically, facilitating comparative studies across different organisms and taxonomic groups.

Secondary Structure Diagrams

Representative RNA secondary structure diagrams are provided, with each base pair validated through comparative sequence analysis. This ensures that the proposed structures are supported by evolutionary evidence.

Structural Information

• 2D Structures: Secondary structure diagrams with conserved motifs
• 3D Structures: Experimentally determined three-dimensional structures
• Models: Computational models of SRP components

Phylogenetic Organization

Sequences are organized phylogenetically, allowing researchers to track evolutionary relationships and conservation patterns across different domains of life.

Historical Significance

The database documents the history of SRP research, including:

• Key publication from 1972
• Commentary from 1999 Nobel Prize winner Günter Blobel
• Connection to the 1999 Nobel Prize in Physiology or Medicine

Methodology

Comparative Sequence Analysis

Base pairs in secondary structure diagrams are validated using comparative sequence analysis, a powerful approach that identifies conserved structural elements based on covariation in aligned sequences.

Annotation

All sequences are manually annotated and curated, with special attention to:

• Conserved sequence motifs
• Functional domains
• Phylogenetic relationships
• Structural features

Mirror Sites

SRPDB is maintained with mirror sites in:

• Sweden: University of Gothenburg
• Denmark: University of Copenhagen (Rigshospitalet)

Associates

SRPDB is maintained through collaboration with experts from:

• Ebbe Andersen (Aarhus University, Biodesign)
• Jan Gorodkin (University of Copenhagen)
• Niels Larsen (Genomics)
• Magnus Alm Rosenblad (University of Gothenburg)
• Tore Samuelsson (University of Gothenburg)
• Christian Zwieb (University of Texas Health Science Center at San Antonio)

Acknowledgments

SRPDB development was supported by:

• National Institutes of Health
• Danish Technical Research Council
• Contributions from ERNA-3D modeling software (Florian Müller)
• VCMD molecular dynamics software (Ingolf Sommer)

Citation

If your research is assisted by SRPDB, please cite:

• Andersen ES, et al. (2006) The tmRDB and SRPDB Resources. Nucleic Acids Res. 34, Database issue: D163-168.
• Rosenblad MA, et al. (2009) Kinship in the SRP RNA family. RNA Biol. 6, 508-516.

Please also cite original authors when using redistributed data.

Contact

For questions, data submissions, or suggestions about SRPDB, contact:

• Christian Zwieb, Department of Biochemistry, University of Texas Health Science Center at San Antonio

For specific questions, contact SRPDB Associates listed above.

Last Updated: November 04, 2010