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Open data
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Basic information
| Entry | Database: PDB / ID: 6sli | ||||||
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| Title | Structure of the RagAB peptide transporter | ||||||
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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: 3.38 Å | ||||||
Authors | Madej, M. / Ranson, N.A. / White, J.B.R. | ||||||
Citation | Journal: Nat Microbiol / Year: 2020Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6sli.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb6sli.ent.gz | 1.8 MB | Display | PDB format |
| PDBx/mmJSON format | 6sli.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6sli_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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| Full document | 6sli_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | 6sli_validation.xml.gz | 196.5 KB | Display | |
| Data in CIF | 6sli_validation.cif.gz | 261.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6sli ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6sli | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6sljC ![]() 6slnC ![]() 6sm3C ![]() 6smlC ![]() 6smqC ![]() 5cx8S ![]() 5fq8S S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
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Porphyromonas gingivalis (bacteria)
X-RAY DIFFRACTION
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