Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

Abstract

The Protein Data Bank (PDB)—the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes—was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Identification of compounds that inhibit the binding of Keap1a/Keap1b Kelch DGR domain with Nrf2 ETGE/DLG motifs in zebrafish

“…The crystal structures of the DGR domain and whole Keap1a or Keap1b protein of zebrafish have not been available so far. In order to model the DGR domains of both zebrafish Keap1a and Keap1b proteins, BLAST was performed against the protein data bank (PDB) . So far, no crystal structure has been available for human Keap1.…”

“…In order to model the DGR domains of both zebrafish Keap1a and Keap1b proteins, BLAST was performed against the protein data bank (PDB). 32,33 So far, no crystal structure has been available for human Keap1. From the BLAST analysis, the crystal structure from Mus musculus (PDB ID: 5CGJ) was chosen as a template for homology modelling of DGR domains of both zebrafish Keap1a and Keap1b proteins.…”

Glycoinformatics: Bridging Isolated Islands in the Sea of Data

“…Among the largest modern databases,t here are Glycosciences.de (includes CCSD data, together with NMR spectra, theoretical and empirical 3D structures,a nd data analysis tools); [2] UniCarbKB (successor of the EurocarbDB design study [8] which is focused on eukaryotic glycans,i ncluding the data from GlycoSuite, [9] as well as HPLC,M S, and NMR experimental data); [3] Japan Consortium for Glycobiology and Glycotechnology (JCGG/ACGG collection of functioncentered databases;i ncludes data on glycoproteins and glycome-associated diseases,a nd analytical data); [10] KEGG Glycan (glycan structures,b iomedical and other data from Kyoto Encyclopedia of Genes and Genomes); [4] theC arbohydrate Structure Database (CSDB;p rovides structural, taxonomic,N MR spectroscopic and other information on bacterial, fungal and plant saccharides;includes various data analysis tools); [5] the secondary database GlyTouCan (structural glycan repository created for assigning au nique id to each carbohydrate structure); [11] and some others, [12] such as the Protein Data Bank (PDB;contains 3D structures of some glycans from glycoproteins). [13] Except for rare dedicated databases (such as Escherichia coli oriented ECODAB), [14] most of these databases deposit glycans of mammalian origin. Currently,C SDB [5] (which is developed by the authors of this Viewpoint) provides the most complete coverage on carbohydrates of prokaryotes.I t should be noted that none of the projects ensures the full coverage on natural carbohydrates,and only afew of them are curated.…”

Best practice data life cycle approaches for the life sciences

“…National and international-level organisations of this kind include the European Bioinformatics Institute (EMBL-EBI) 25 , the National Centre for Biotechnology Information (NCBI) 26 , the DNA Data Bank of Japan (DDBJ) 27 , the Swiss Institute of Bioinformatics (SIB) 28 , and the four data center members of the worldwide Protein Data Bank 29 , which mirror their shared data with regular, frequent updates. This shared central infrastructure is hugely valuable to research and development.…”