+Open data
-Basic information
Entry | Database: PDB / ID: 6slj | ||||||
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Title | Structure of the RagAB peptide transporter | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / outer membrane protein / Bacteroidetes / TonB dependent transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Porphyromonas gingivalis (bacteria) Porphyromonas gingivalis W83 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å | ||||||
Authors | Madej, M. / Ranson, N.A. / White, J.B.R. | ||||||
Citation | Journal: Nat Microbiol / Year: 2020 Title: Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Authors: Mariusz Madej / Joshua B R White / Zuzanna Nowakowska / Shaun Rawson / Carsten Scavenius / Jan J Enghild / Grzegorz P Bereta / Karunakar Pothula / Ulrich Kleinekathoefer / Arnaud Baslé / ...Authors: Mariusz Madej / Joshua B R White / Zuzanna Nowakowska / Shaun Rawson / Carsten Scavenius / Jan J Enghild / Grzegorz P Bereta / Karunakar Pothula / Ulrich Kleinekathoefer / Arnaud Baslé / Neil A Ranson / Jan Potempa / Bert van den Berg / Abstract: Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory ...Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagAB complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6slj.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6slj.ent.gz | 903.5 KB | Display | PDB format |
PDBx/mmJSON format | 6slj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6slj ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slj | HTTPS FTP |
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-Related structure data
Related structure data | 6sliSC 6slnC 6sm3C 6smlC 6smqC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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