PDBTM
Protein Data Bank of Transmembrane Proteins
Sat 28 Jan, 2012  1550 TM structures Version 2.3 81520 visitors.
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Welcome to the PDBTM, the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB). PDBTM database is maintained in the Institute of Enzymology by the Protein Structure Research Group. PDBTM database was created by scanning all PDB entries with TMDET algorithm. You can read more about PDBTM in our articles and in PDBTM manual. If you find PDBTM useful in your research, please cite our articles (Bioinformatics 20, 2964-2972; Nucleic Acids Research 33 Database Issue, D275-8).

Current holdings
  • 79538 structures,
  • 1550 transmembrane structures,
    • 1330 alpha helical,
    • 219 beta barrel.

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PDBTM database is updated in a semi-automated mode in every week. Last update was on 12 Jan, 2012

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2005-08-20
New web design and content for PDBTM database.
2005-07-20
TMDET version 2.0 was applied on all PDBTM entries.
Molecule of the month
FIMD translocation domain


3ohn

Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyses their polymerization and mediates pilus translocation across the outer membrane. In article of Nature Here we report the crystal structure of the full-length FimD usher bound to the FimC-FimH chaperone-adhesin complex and that of the unbound form of the FimD translocation domain. The FimD-FimC-FimH structure shows FimH inserted inside the FimD 24-stranded β-barrel translocation channel. FimC-FimH is held in place through interactions with the two carboxy-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a marked conformational change in the β-barrel. The amino-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone-subunit complex. The FimD-FimC-FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.