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Open data
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Basic information
Entry | Database: PDB / ID: 6sml | ||||||||||||||||||||||||
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Title | Structure of the RagAB peptide importer in the 'open-open' state | ||||||||||||||||||||||||
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![]() | MEMBRANE PROTEIN / Beta-barrel / OMP / TonB-dependent / transporter | ||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||||||||
![]() | White, J.B.R. / Ranson, N.A. / van den Berg, B. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.3 KB | Display | ![]() |
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PDB format | ![]() | 267.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10243MC ![]() 6sliC ![]() 6sljC ![]() 6slnC ![]() 6sm3C ![]() 6smqC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data size: 9.0 TB Data #1: Raw micrograph movies of the RagAB complex solubilised in DDM [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Components
#1: Protein | Mass: 54430.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 101582.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein/peptide | Mass: 952.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Putative peptide substrate / Source: (natural) ![]() |
#4: Chemical | ChemComp-5PL / ( |
#5: Chemical | ChemComp-PLM / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RagAB with putative peptide substrate / Type: COMPLEX Details: Putative peptide substrate co-purified with the complex Entity ID: #1-#3 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279.15 K / Details: 6 second blot time, blot force 6 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 77.88 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51849 / Symmetry type: POINT |