Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.
Journal, issue, pages	Nat Microbiol, Vol. 5, Issue 8, Page 1016-1025, Year 2020
Publish date	May 11, 2020
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 /
PubMed 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.
External links	Nat Microbiol / PubMed:32393857 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.61 - 3.4 Å
Structure data	10241 6sm3 EMDB-10241, PDB-6sm3: Structure of the RagAB peptide importer in the 'closed-closed' state Method: EM (single particle) / Resolution: 3.3 Å 10243 6sml EMDB-10243, PDB-6sml: Structure of the RagAB peptide importer in the 'open-open' state Method: EM (single particle) / Resolution: 3.4 Å 10245 6smq EMDB-10245, PDB-6smq: Structure of the RagAB peptide importer in the 'open-closed' state Method: EM (single particle) / Resolution: 3.3 Å PDB-6sli: Structure of the RagAB peptide transporter Method: X-RAY DIFFRACTION / Resolution: 3.38 Å PDB-6slj: Structure of the RagAB peptide transporter Method: X-RAY DIFFRACTION / Resolution: 3.04 Å PDB-6sln: Structure of the RagAB peptide transporter Method: X-RAY DIFFRACTION / Resolution: 2.61 Å
Chemicals	ChemComp-5PL: (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE ChemComp-C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE / C8E, detergentYM ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM / Phosphatidylethanolamine ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-PLM: PALMITIC ACID / Palmitic acid ChemComp-HOH*: WATER / Water
Source	porphyromonas gingivalis w83 (bacteria) porphyromonas gingivalis (strain atcc baa-308 / w83) (bacteria)
Keywords	MEMBRANE PROTEIN / outer membrane protein / Bacteroidetes / TonB dependent transporter / Beta-barrel / OMP / TonB-dependent / transporter