+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9909 | |||||||||||||||
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Title | Salmonella hook in curved state - unsymmetrized cryo-EM map | |||||||||||||||
Map data | full map | |||||||||||||||
Sample |
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Keywords | bacterial / hook / flexible joint / flagella / MOTOR PROTEIN | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||||||||
Authors | Shibata S / Matsunami H | |||||||||||||||
Funding support | Japan, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM. Authors: Satoshi Shibata / Hideyuki Matsunami / Shin-Ichi Aizawa / Matthias Wolf / Abstract: Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, ...Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, yet it adopts a curved shape. To perform its function, it must be simultaneously flexible and torsionally rigid. The molecular mechanism by which chemically identical subunits form such a dynamic structure is unknown. Here, we show the complete structure of the hook from Salmonella enterica in its supercoiled 'curved' state, at 2.9 Å resolution. Subunits in the curved hook are grouped into 11 distinctive conformations, each shared along 11 protofilaments. The domains of the elongated hook subunit behave as rigid bodies connected by two hinge regions. The reconstituted model demonstrates how identical subunits can dynamically change conformation by physical interactions while bending. These multiple subunit states contradict the two-state model, which is a key feature of flagellar polymorphism. | |||||||||||||||
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_9909.map.gz | 200.2 MB | EMDB map data format | |
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Header (meta data) | emd-9909-v30.xml emd-9909.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9909_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_9909.png | 265.7 KB | ||
Filedesc metadata | emd-9909.cif.gz | 5.9 KB | ||
Others | emd_9909_half_map_1.map.gz emd_9909_half_map_2.map.gz | 72.7 MB 72.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9909 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9909 | HTTPS FTP |
-Validation report
Summary document | emd_9909_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_9909_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_9909_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_9909_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9909 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9909 | HTTPS FTP |
-Related structure data
Related structure data | 6k3iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9909.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_9909_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_9909_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacterial flagellar polyhook
Entire | Name: Bacterial flagellar polyhook |
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Components |
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-Supramolecule #1: Bacterial flagellar polyhook
Supramolecule | Name: Bacterial flagellar polyhook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 2.8 MDa |
-Macromolecule #1: Flagellar hook protein FlgE
Macromolecule | Name: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 66 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 42.101957 KDa |
Sequence | String: SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP ...String: SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP FSVSDADSYN KKGTVTVYDS QGNAHDMNVY FVKTKDNEWA VYTHDSSDPA ATAPTTASTT LKFNENGILE SG GTVNITT GTINGATAAT FSLSFLNSMQ QNTGANNIVA TNQNGYKPGD LVSYQINNDG TVVGNYSNEQ EQVLGQIVLA NFA NNEGLA SQGDNVWAAT QASGVALLGT AGSGNFGKLT NGALEASNVD LSKELVNMIV AQRNYQSNAQ TIKTQDQILN TLVN LR UniProtKB: Flagellar hook protein FlgE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 3.5 / Component - Concentration: 50.0 mM / Component - Formula: C2H5NO2 / Component - Name: Glycine |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 4.0uL. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 100.0 K |
Details | nanoprobe, parallel beam illumination |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 2655 / Average exposure time: 2.0 sec. / Average electron dose: 89.0 e/Å2 Details: frame alignment and dose weighting using motioncor2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.13 µm / Calibrated defocus min: 0.43 µm / Calibrated magnification: 107914 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.13 µm / Nominal defocus min: 0.43 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |