Cryo electron microscopy of RagAB from P. gingivalis solubilised in DDM
Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Baslé A, Ranson NA, Potempa J, van den Berg B
Nat Microbiol (2020) 5 pp. 1016-1025 [ Pubmed: 32393857 DOI: 10.1038/s41564-020-0716-y ]
Image sets:
Structure of the RagAB peptide importer in the 'closed-closed' state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6sm3
Q-score: 0.585
Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B
Nat Microbiol (2020) 5 pp. 1016-1025 [ DOI: doi:10.1038/s41564-020-0716-y Pubmed: 32393857 ]
- Ragab with putative peptide substrate (Complex from Porphyromonas gingivalis W83)
- Gly-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-thr-ser (1 kDa, Protein from Porphyromonas gingivalis W83)
- Lipoprotein ragb (54 kDa, Protein from Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
- (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 (1 kDa, Ligand)
- Raga protein (100 kDa, Protein from Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
- Palmitic acid (256 Da, Ligand)
Structure of the RagAB peptide importer in the 'open-open' state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6sml
Q-score: 0.559
Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B
Nat Microbiol (2020) 5 pp. 1016-1025 [ DOI: doi:10.1038/s41564-020-0716-y Pubmed: 32393857 ]
- (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 (1 kDa, Ligand)
- Gly-thr-gly-gly-ser-thr-gly-thr-thr-ser-ala-gly (952 Da, Protein from Porphyromonas gingivalis W83)
- Palmitic acid (256 Da, Ligand)
- Raga protein (101 kDa, Protein from Porphyromonas gingivalis W83)
- Lipoprotein ragb (54 kDa, Protein from Porphyromonas gingivalis W83)
- Ragab with putative peptide substrate (Complex from Porphyromonas gingivalis W83)
Structure of the RagAB peptide importer in the 'open-closed' state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6smq
Q-score: 0.587
Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B
Nat Microbiol (2020) 5 pp. 1016-1025 [ DOI: doi:10.1038/s41564-020-0716-y Pubmed: 32393857 ]
- Palmitic acid (256 Da, Ligand)
- Ragab with putative peptide substrate (Complex from Porphyromonas gingivalis W83)
- Raga protein (101 kDa, Protein from Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
- Lipoprotein ragb (54 kDa, Protein from Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
- (hydroxyethyloxy)tri(ethyloxy)octane (306 Da, Ligand)
- (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 (1 kDa, Ligand)
- Raga protein (100 kDa, Protein from Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
- Ser-gly-ala-thr-thr-ala-thr-thr-thr-thr-ser-asn-ser (1 kDa, Protein from Porphyromonas gingivalis W83)