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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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The Protein Data Bank Archive.

Sameer Velankar1, Stephen K Burley2,3,4,5, Genji Kurisu6

  • 1Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK. sameer@ebi.ac.uk.

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|May 5, 2021
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank (PDB) archive, managed by the worldwide Protein Data Bank (wwPDB), provides open access to experimentally determined macromolecular structures. It ensures data quality and accessibility through continuous development and adherence to FAIR principles.

Keywords:
3DEMBiocuration, and Validation system OneDepDepositionIntegrative hybrid methodsMacromolecular structure archiveNMR spectroscopyPDBx/mmCIFProtein Data BankValidation task forcesWorldwide Protein Data Bank (wwPDB)X-ray crystallography

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) is the primary global repository for experimentally determined macromolecular structures.
  • Established in 1971, it pioneered open access data in biology.
  • Managed by the worldwide Protein Data Bank (wwPDB) consortium, it comprises four major partners.

Purpose of the Study:

  • To describe the current state and ongoing developments of the PDB archive.
  • To highlight the wwPDB's commitment to data quality, standardization, and accessibility.
  • To outline the resources and data provided within each PDB entry.

Main Methods:

  • Data deposition, biocuration, and validation through the OneDep system.
  • Community-driven task forces and working groups for data standards.
  • Development of data access and analysis tools by wwPDB partners.

Main Results:

  • The PDB archive contains approximately 175,000 entries.
  • Over 250 new entries are added weekly, ensuring up-to-date structural information.
  • Each entry includes atomic coordinates, metadata, experimental data, validation reports, and quaternary structure information.

Conclusions:

  • The wwPDB actively promotes FAIR data principles (Findability, Accessibility, Interoperability, Reproducibility).
  • Ongoing efforts focus on accommodating new techniques like 3D Electron Microscopy (3DEM) and integrative/hybrid methods.
  • The PDB archive remains a vital, evolving resource for the scientific community.