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Yorodumi- EMDB-10561: Structure of the RBM3/collar region of the Salmonella flagella MS... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10561 | |||||||||||||||||||||
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Title | Structure of the RBM3/collar region of the Salmonella flagella MS-ring protein FliF with 35-fold symmetry applied | |||||||||||||||||||||
Map data | Post process map | |||||||||||||||||||||
Sample |
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Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||||||||
Authors | Johnson S / Fong YH / Deme JC / Furlong EJ / Kuhlen L / Lea SM | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation. Authors: Steven Johnson / Yu Hang Fong / Justin C Deme / Emily J Furlong / Lucas Kuhlen / Susan M Lea / Abstract: The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical ...The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical propeller that is attached to a motor embedded in the inner membrane. The motor consists of a series of stator units surrounding a central rotor made up of two ring complexes, the MS-ring and the C-ring. Despite many studies, high-resolution structural information is still lacking for the MS-ring of the rotor, and proposed mismatches in stoichiometry between the two rings have long provided a source of confusion for the field. Here, we present structures of the Salmonella MS-ring, revealing a high level of variation in inter- and intrachain symmetry that provides a structural explanation for the ability of the MS-ring to function as a complex and elegant interface between the two main functions of the flagellum-protein secretion and rotation. | |||||||||||||||||||||
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_10561.map.gz | 36.3 MB | EMDB map data format | |
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Header (meta data) | emd-10561-v30.xml emd-10561.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10561_fsc.xml | 15.4 KB | Display | FSC data file |
Images | emd_10561.png | 46.7 KB | ||
Masks | emd_10561_msk_1.map | 307.5 MB | Mask map | |
Others | emd_10561_additional.map.gz emd_10561_additional_1.map.gz emd_10561_half_map_1.map.gz emd_10561_half_map_2.map.gz | 237.9 MB 237.9 MB 243.5 MB 243.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10561 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10561 | HTTPS FTP |
-Validation report
Summary document | emd_10561_validation.pdf.gz | 405.6 KB | Display | EMDB validaton report |
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Full document | emd_10561_full_validation.pdf.gz | 404.7 KB | Display | |
Data in XML | emd_10561_validation.xml.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10561 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10561 | HTTPS FTP |
-Related structure data
Related structure data | 6scnC 6sd1C 6sd2C 6sd3C 6sd4C 6sd5C 6treC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10561.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post process map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10561_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Refinement map
File | emd_10561_additional.map | ||||||||||||
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Annotation | Refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Refinement map
File | emd_10561_additional_1.map | ||||||||||||
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Annotation | Refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_10561_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_10561_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
Entire | Name: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF |
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Components |
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-Supramolecule #1: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
Supramolecule | Name: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 |
Molecular weight | Theoretical: 2.14 MDa |
-Macromolecule #1: Flagellar MS-ring FliF
Macromolecule | Name: Flagellar MS-ring FliF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQ LTQMNIPYRF ANGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE K FGISQFSE QVNYQRALEG ELARTIETLG PVKSARVHLA MPKPSLFVRE ...String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQ LTQMNIPYRF ANGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE K FGISQFSE QVNYQRALEG ELARTIETLG PVKSARVHLA MPKPSLFVRE QKSPSASVTV TL EPGRALD EGQISAVVHL VSSAVAGLPP GNVTLVDQSG HLLTQSNTSG RDLNDAQLKF AND VESRIQ RRIEAILSPI VGNGNVHAQV TAQLDFANKE QTEEHYSPNG DASKATLRSR QLNI SEQVG AGYPGGVPGA LSNQPAPPNE APIATPPTNQ QNAQNTPQTS TSTNSNSAGP RSTQR NETS NYEVDRTIRH TKMNVGDIER LSVAVVVNYK TLADGKPLPL TADQMKQIED LTREAM GFS DKRGDTLNVV NSPFSAVDNT GGELPFWQQQ SFIDQLLAAG RWLLVLVVAW ILWRKAV RP QLTRRVEEAK AAQEQAQVRQ ETEEAVEVRL SKDEQLQQRR ANQRLGAEVM SQRIREMS D NDPRVVALVI RQWMSNDHE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |