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- EMDB-10245: Structure of the RagAB peptide importer in the 'open-closed' state -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10245 | ||||||||||||||||||||||||
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Title | Structure of the RagAB peptide importer in the 'open-closed' state | ||||||||||||||||||||||||
![]() | Sharpened map filtered by local resolution in RELION | ||||||||||||||||||||||||
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Function / homology | ![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
![]() | White JBR / Ranson NA / 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.7 KB 26.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.8 KB | Display | ![]() |
Images | ![]() | 59.7 KB | ||
Masks | ![]() | 38.4 MB | ![]() | |
Others | ![]() ![]() ![]() | 29.4 MB 14.7 MB 14.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6smqMC ![]() 6sliC ![]() 6sljC ![]() 6slnC ![]() 6sm3C ![]() 6smlC C: citing same article ( M: atomic model generated by this map |
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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
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map filtered by local resolution in RELION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map from 3D auto-refinement in RELION
File | emd_10245_additional_1.map | ||||||||||||
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Annotation | Unsharpened map from 3D auto-refinement in RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map 1 from final iteration of 3D auto-refinement in RELION
File | emd_10245_additional_2.map | ||||||||||||
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Annotation | Half map 1 from final iteration of 3D auto-refinement in RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map 2 from final iteration of 3D auto-refinement in RELION
File | emd_10245_additional_3.map | ||||||||||||
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Annotation | Half map 2 from final iteration of 3D auto-refinement in RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RagAB with putative peptide substrate
Entire | Name: RagAB with putative peptide substrate |
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Components |
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-Supramolecule #1: RagAB with putative peptide substrate
Supramolecule | Name: RagAB with putative peptide substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Putative peptide substrate co-purified with the complex |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Lipoprotein RagB
Macromolecule | Name: Lipoprotein RagB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-308 / W83 |
Molecular weight | Theoretical: 54.430863 KDa |
Sequence | String: CELDRDPEGK DFQQPYTSFV QTKQNRDGLY ALLRNTENPR MHFYQELQSD MYCTTITDGN SLAPFVNWDL GILNDHGRAD EDEVSGIAG YYFVYNRLNQ QANAFVNNTE AALQNQVYKN STEIANAKSF LAEGKVLQAL AIWRLMDRFS FHESVTEVNS G AKDLGVIL ...String: CELDRDPEGK DFQQPYTSFV QTKQNRDGLY ALLRNTENPR MHFYQELQSD MYCTTITDGN SLAPFVNWDL GILNDHGRAD EDEVSGIAG YYFVYNRLNQ QANAFVNNTE AALQNQVYKN STEIANAKSF LAEGKVLQAL AIWRLMDRFS FHESVTEVNS G AKDLGVIL LKEYNPGYIG PRATKAQCYD YILSRLSEAI EVLPENRESV LYVSRDYAYA LRARIYLALG EYGKAAADAK MV VDKYPLI GAADASEFEN IYRSDANNPE IIFRGFASAT LGSFTATTLN GAAPAGKDIK YNPSAVPFQW VVDLYENEDF RKS VYIAKV VKKDKGYLVN KFLEDKAYRD VQDKPNLKVG ARYFSVAEVY LILVESALQT GDTPTAEKYL KALSKARGAE VSVV NMEAL QAERTRELIG EGSRLRDMVR WSIPNNHDAF ETQPGLEGFA NTTPLKAQAP VGFYAYTWEF PQRDRQTNPQ LIKNW PI |
-Macromolecule #2: RagA protein
Macromolecule | Name: RagA protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-308 / W83 |
Molecular weight | Theoretical: 100.350977 KDa |
Sequence | String: LSTVSGSVAK VSSEKLAEKP VANIMDALQG QVAGMQVMTT SGDPTAVASV EIHGTGSLGA SSAPLYIVDG MQTSLDVVAT MNPNDFESM SVLKDASATS IYGARAANGV VFIQTKKGKM SERGRITFNA SYGISQILNT KPLDNMMTGD ELLDFQVKAG F WGNNQTVQ ...String: LSTVSGSVAK VSSEKLAEKP VANIMDALQG QVAGMQVMTT SGDPTAVASV EIHGTGSLGA SSAPLYIVDG MQTSLDVVAT MNPNDFESM SVLKDASATS IYGARAANGV VFIQTKKGKM SERGRITFNA SYGISQILNT KPLDNMMTGD ELLDFQVKAG F WGNNQTVQ KVKDMILAGA EDLYGNYDSL KDEYGKTLFP VDFNHDADWL KALFKTAPTS QGDISFSGGS QGTSYYASIG YF DQEGMAR EPANFKRYSG RLNFESRINE WLKVGANLSG AIANRRSADY FGKYYMGSGT FGVLTMPRYY NPFDVNGDLA DVY YMYGAT RPSMTEPYFA KMRPFSSESH QANVNGFAQI TPIKGLTLKA QAGVDITNTR TSSKRMPNNP YDSTPLGERR ERAY RDVSK SFTNTAEYKF SIDEKHDLTA LMGHEYIEYE GDVIGASSKG FESDKLMLLS QGKTGNSLSL PEHRVAEYAY LSFFS RFNY GFDKWMYIDF SVRNDQSSRF GSNNRSAWFY SVGGMFDIYN KFIQESNWLS DLRLKMSYGT TGNSEIGNYN HQALVT VNN YTEDAMGLSI STAGNPDLSW EKQSQFNFGL AAGAFNNRLS AEVDFYVRTT NDMLIDVPMP YISGFFSQYQ NVGSMKN TG VDLSLKGTIY QNKDWNVYAS ANFNYNRQEI TKLFFGLNKY MLPNTGTIWE IGYPNSFYMA EYAGIDKKTG KQLWYVPG Q VDADGNKVTT SQYSADLETR IDKSVTPPIT GGFSLGASWK GLSLDADFAY IVGKWMINND RYFTENGGGL MQLNKDKML LNAWTEDNKE TDVPKLGQSP QFDTHLLENA SFLRLKNLKL TYVLPNSLFA GQNVIGGARV YLMARNLLTV TKYKGFDPEA GGNVGKNQY PNSKQYVAGI QLSF |
-Macromolecule #3: SER-GLY-ALA-THR-THR-ALA-THR-THR-THR-THR-SER-ASN-SER
Macromolecule | Name: SER-GLY-ALA-THR-THR-ALA-THR-THR-THR-THR-SER-ASN-SER / type: protein_or_peptide / ID: 3 / Details: Putative peptide ligand / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.199182 KDa |
Sequence | String: SGATTATTTT SNS |
-Macromolecule #4: RagA protein
Macromolecule | Name: RagA protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-308 / W83 |
Molecular weight | Theoretical: 101.582398 KDa |
Sequence | String: QVVVLGYGTG QKLSTVSGSV AKVSSEKLAE KPVANIMDAL QGQVAGMQVM TTSGDPTAVA SVEIHGTGSL GASSAPLYIV DGMQTSLDV VATMNPNDFE SMSVLKDASA TSIYGARAAN GVVFIQTKKG KMSERGRITF NASYGISQIL NTKPLDNMMT G DELLDFQV ...String: QVVVLGYGTG QKLSTVSGSV AKVSSEKLAE KPVANIMDAL QGQVAGMQVM TTSGDPTAVA SVEIHGTGSL GASSAPLYIV DGMQTSLDV VATMNPNDFE SMSVLKDASA TSIYGARAAN GVVFIQTKKG KMSERGRITF NASYGISQIL NTKPLDNMMT G DELLDFQV KAGFWGNNQT VQKVKDMILA GAEDLYGNYD SLKDEYGKTL FPVDFNHDAD WLKALFKTAP TSQGDISFSG GS QGTSYYA SIGYFDQEGM AREPANFKRY SGRLNFESRI NEWLKVGANL SGAIANRRSA DYFGKYYMGS GTFGVLTMPR YYN PFDVNG DLADVYYMYG ATRPSMTEPY FAKMRPFSSE SHQANVNGFA QITPIKGLTL KAQAGVDITN TRTSSKRMPN NPYD STPLG ERRERAYRDV SKSFTNTAEY KFSIDEKHDL TALMGHEYIE YEGDVIGASS KGFESDKLML LSQGKTGNSL SLPEH RVAE YAYLSFFSRF NYGFDKWMYI DFSVRNDQSS RFGSNNRSAW FYSVGGMFDI YNKFIQESNW LSDLRLKMSY GTTGNS EIG NYNHQALVTV NNYTEDAMGL SISTAGNPDL SWEKQSQFNF GLAAGAFNNR LSAEVDFYVR TTNDMLIDVP MPYISGF FS QYQNVGSMKN TGVDLSLKGT IYQNKDWNVY ASANFNYNRQ EITKLFFGLN KYMLPNTGTI WEIGYPNSFY MAEYAGID K KTGKQLWYVP GQVDADGNKV TTSQYSADLE TRIDKSVTPP ITGGFSLGAS WKGLSLDADF AYIVGKWMIN NDRYFTENG GGLMQLNKDK MLLNAWTEDN KETDVPKLGQ SPQFDTHLLE NASFLRLKNL KLTYVLPNSL FAGQNVIGGA RVYLMARNLL TVTKYKGFD PEAGGNVGKN QYPNSKQYVA GIQLSF |
-Macromolecule #5: (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OX...
Macromolecule | Name: (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 type: ligand / ID: 5 / Number of copies: 2 / Formula: 5PL |
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Molecular weight | Theoretical: 1.233719 KDa |
Chemical component information | ![]() ChemComp-5PL: |
-Macromolecule #6: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Macromolecule #7: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Macromolecule | Name: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE / type: ligand / ID: 7 / Number of copies: 5 / Formula: C8E |
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Molecular weight | Theoretical: 306.438 Da |
Chemical component information | ![]() ChemComp-C8E: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.75 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV / Details: 6 second blot time, blot force 6. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 77.88 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |