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Yorodumi- EMDB-10894: PorLM complex from Porphyromonas gingivalis solubilised in LMNG m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10894 | ||||||||||||
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Title | PorLM complex from Porphyromonas gingivalis solubilised in LMNG micelle | ||||||||||||
Map data | Volume of full length PorLM in LMNG micelle | ||||||||||||
Sample |
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Biological species | Flavobacterium johnsoniae (bacteria) / Porphyromonas gingivalis (bacteria) / Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | ||||||||||||
Authors | Hennell James R / Deme JC / Lea SM | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Microbiol / Year: 2021 Title: Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Authors: Rory Hennell James / Justin C Deme / Andreas Kjӕr / Felicity Alcock / Augustinas Silale / Frédéric Lauber / Steven Johnson / Ben C Berks / Susan M Lea / Abstract: Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein ...Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM from Porphyromonas gingivalis. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM/PorM proteins are positioned inside a ring of five GldL/PorL proteins. Mutagenesis and single-molecule tracking identify protonatable amino acid residues in the transmembrane domain of the complex that are important for motor function. Our data provide evidence for a mechanism in which proton flow results in rotation of the periplasm-spanning GldM/PorM dimer inside the intra-membrane GldL/PorL ring to drive processes at the bacterial outer membrane. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10894.map.gz | 332.3 MB | EMDB map data format | |
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Header (meta data) | emd-10894-v30.xml emd-10894.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_10894.png | 32.4 KB | ||
Masks | emd_10894_msk_1.map | 421.9 MB | Mask map | |
Others | emd_10894_half_map_1.map.gz emd_10894_half_map_2.map.gz | 338.5 MB 338.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10894 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10894 | HTTPS FTP |
-Validation report
Summary document | emd_10894_validation.pdf.gz | 288.9 KB | Display | EMDB validaton report |
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Full document | emd_10894_full_validation.pdf.gz | 288 KB | Display | |
Data in XML | emd_10894_validation.xml.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10894 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10894 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10894.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Volume of full length PorLM in LMNG micelle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10894_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_10894_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_10894_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PorLM
Entire | Name: PorLM |
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Components |
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-Supramolecule #1: PorLM
Supramolecule | Name: PorLM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: PorL
Macromolecule | Name: PorL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyromonas gingivalis (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGF EKPAMEYHWE EVFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERSSS V RLASASLG TQPQEQSKPA TPFQSQLTGI LPEEQIQRLS EGIDKLAEAG ...String: MGHYRRYKNI LEMYLASHKG RRLLNIVYSW GAAVVILGAL FKLLHLPMGN EMLFVGMITE FLVFFISGF EKPAMEYHWE EVFPELDSKN PMDRREMEQR REYLREKAKE AAAYAERSSS V RLASASLG TQPQEQSKPA TPFQSQLTGI LPEEQIQRLS EGIDKLAEAG EQLARIGRTA AA MTESYEQ MQADQEGLRL NSQSYIQQME SLSRNISGLN TIYEIQLKGI SSQIDTIDRI NRG LAHIRD MYDNSVIDSS SFRNENERMA RQLTQLNEVY ARLLQALTTN VGLPGMPGNF GASN PSSSG SSPL |
-Macromolecule #2: PorM
Macromolecule | Name: PorM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria) |
Sequence | String: MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRT NPEKVKVWYE RSLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK D NLDASSVV MLNPINGKGS TLRKEVDKFR ELVATLMTDK AKLKLIEQAL ...String: MAVGSNGNAN RQKMINLMYL VFIAMMALNV SSEVLDGFDK VDKSLTSSID GSDKRNNLVL SELNTAYRT NPEKVKVWYE RSLVLQKEAD SLCTFIDDLK LAIARESDGK DAKVNDIRRK D NLDASSVV MLNPINGKGS TLRKEVDKFR ELVATLMTDK AKLKLIEQAL NTESGTKGKS WE SSLFENM PTVAAITLLT KLQSDVRYAQ GEVLADLVKS VDVGDYRVNS ITAQVIPQSQ IVM SGDTYK ANIVLSSVDT TQRPDVFVNG KLLSPENMGL FTATAGAPGT YPVKGYIEMM GNDG VKIRR DFESEYFVTE PMASVAPTMM NVLYAGIDNP INIAVPGVAQ QNVSATINNG TLTRR GNLW IARPTKVGSE AIISVTAQSG GRTIQMAKTT LRVRALPDPL PYIEYKDVQG NTKRFK GGR LGKREILAAG GIKAALDDDL LEVNYTVVKF QLVFYDSMGN SIPEVSDGAS FSERQKR QI QNLGKGKRFY VTEVIARGPD GIERKIPAIE VIVN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0003 µm / Nominal defocus min: 0.0001 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |