+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9952 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the native supercoiled hook as a universal joint | |||||||||||||||
Map data | ||||||||||||||||
Sample |
| |||||||||||||||
Keywords | Flagella motor / Hook / Native structure / Supercoiled / FlgE / MOTOR PROTEIN | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum-dependent cell motility Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Salmonella typhimurium (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Kato T / Miyata T | |||||||||||||||
Funding support | Japan, 4 items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structure of the native supercoiled flagellar hook as a universal joint. Authors: Takayuki Kato / Fumiaki Makino / Tomoko Miyata / Péter Horváth / Keiichi Namba / Abstract: The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body ...The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body and filament, and smoothly transmits torque generated by the rotary motor to the helical filament propeller. In peritrichously flagellated bacteria, the hook allows the filaments to form a bundle behind the cell for swimming, and for the bundle to fall apart for tumbling. Here we report a native supercoiled hook structure at 3.6 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built into the three-dimensional (3D) density map reveals the changes in subunit conformation and intersubunit interactions that occur upon compression and extension of the 11 protofilaments during their smoke ring-like rotation. These observations reveal how the hook functions as a dynamic molecular universal joint with high bending flexibility and twisting rigidity. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9952.map.gz | 116.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9952-v30.xml emd-9952.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9952_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_9952.png | 156.6 KB | ||
Filedesc metadata | emd-9952.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9952 | HTTPS FTP |
-Validation report
Summary document | emd_9952_validation.pdf.gz | 836.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_9952_full_validation.pdf.gz | 835.7 KB | Display | |
Data in XML | emd_9952_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_9952_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9952 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9952 | HTTPS FTP |
-Related structure data
Related structure data | 6k9qMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9952.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.097 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Native supercoiled hook
Entire | Name: Native supercoiled hook |
---|---|
Components |
|
-Supramolecule #1: Native supercoiled hook
Supramolecule | Name: Native supercoiled hook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 42979 kDa/nm |
-Macromolecule #1: Flagellar hook protein FlgE
Macromolecule | Name: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella typhimurium (bacteria) |
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
---|---|
Temperature | Min: 99.7 K / Max: 100.5 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 2-50 / Number grids imaged: 1 / Number real images: 1702 / Average exposure time: 10.0 sec. / Average electron dose: 0.87 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal magnification: 50000 |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||||
Output model | PDB-6k9q: |