Question

Which of the following is a data bank exclusively for proteins?

• A. DDBJ
• B. EMBL
• C. Genbank
• D. PDB

Hint:

• INSDC (GenBank, ENA/EMBL, DDBJ) Primary nucleotide sequence databases.
• UniProt (Swiss-Prot, TrEMBL) Primary protein sequence databases.
• PDB (Protein Data Bank) Database of 3D macromolecular structures (proteins and nucleic acids).
• Pay attention to "sequence" vs. "structure" and "nucleotide" vs. "protein".

Answer 1

The Correct Option is D

Biological sequence and structure databases are essential resources in bioinformatics.

• Nucleotide Sequence Databases: These store DNA and RNA sequence data. The major primary nucleotide sequence databases are:
  • GenBank (Option c): Maintained by NCBI (National Center for Biotechnology Information) in the USA.
  • EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database (Option b): Maintained by EBI (European Bioinformatics Institute). Now part of ENA (European Nucleotide Archive).
  • DDBJ (DNA Data Bank of Japan) (Option a): Maintained in Japan.
  These three databases (GenBank, EMBL/ENA, DDBJ) form the International Nucleotide Sequence Database Collaboration (INSDC) and exchange data daily.
• Protein Sequence Databases:
  • UniProt (Universal Protein Resource): A comprehensive resource for protein sequences and functional information, resulting from the merger of Swiss-Prot, TrEMBL, and PIR-PSD.
    • Swiss-Prot: Manually curated, high-quality protein sequences with rich annotation.
    • TrEMBL: Computationally annotated translations of EMBL/GenBank/DDBJ coding sequences.
  • NCBI Protein database (derived from GenBank translations etc.)
• Protein Structure Databases:
  • PDB (Protein Data Bank) (Option d): The primary international repository for 3D structural data of large biological molecules, including proteins and nucleic acids, determined by methods like X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. While it contains nucleic acid structures too, it is overwhelmingly dominated by protein structures.

The question asks for a data bank "exclusively for proteins." (a) DDBJ: Nucleotide sequences. (b) EMBL: Nucleotide sequences. (c) Genbank: Nucleotide sequences (though it contains coding sequence annotations that translate to proteins). (d) PDB: Primarily 3D structures of proteins (and nucleic acids). If "exclusively for proteins" refers to its main content focus in terms of macromolecules being studied for structure, PDB fits well, although it also has some RNA/DNA structures. If it means primary sequences, then UniProt/Swiss-Prot would be the answer, but they are not options. Among the given options, PDB is the most appropriate answer as its primary focus is on protein (and nucleic acid) 3D structures, and thus implicitly on the proteins themselves as entities with structure. Options a, b, c are definitively nucleotide sequence databases. If "exclusively for proteins" means primary sequence, then this question is poorly optioned. If it means "primarily about protein information (structure in this case)", then PDB. Given the checkmark is on PDB, this latter interpretation is likely. \[ \boxed{\text{PDB (Protein Data Bank - primarily for 3D structures of proteins)}} \]