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Yorodumi- EMDB-37628: Cryo-EM structure of the whole rod-export apparatus with hook wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37628 | ||||||||||||
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Title | Cryo-EM structure of the whole rod-export apparatus with hook within the flagellar motor-hook complex in the CCW state. | ||||||||||||
Map data | Experimental map | ||||||||||||
Sample |
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Keywords | Flagellum / Flagellar motor / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion ...bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting / structural molecule activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Tan JX / Zhang L / Zhou Y / Zhu YQ | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the whole rod-export apparatus with hook within the flagellar motor-hook complex in the CCW state. Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37628.map.gz | 483.3 MB | EMDB map data format | |
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Header (meta data) | emd-37628-v30.xml emd-37628.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37628_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_37628.png | 62.5 KB | ||
Filedesc metadata | emd-37628.cif.gz | 7.7 KB | ||
Others | emd_37628_half_map_1.map.gz emd_37628_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37628 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37628 | HTTPS FTP |
-Validation report
Summary document | emd_37628_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_37628_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_37628_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | emd_37628_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37628 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37628 | HTTPS FTP |
-Related structure data
Related structure data | 8wlqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37628.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Experimental map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.332 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_37628_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_37628_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : C ring-containing flagellar motor-hook complex in the CCW state
+Supramolecule #1: C ring-containing flagellar motor-hook complex in the CCW state
+Macromolecule #1: Flagellar basal-body rod protein FlgG
+Macromolecule #2: Flagellar hook protein FlgE
+Macromolecule #3: Flagellar biosynthetic protein FliQ
+Macromolecule #4: Flagellar biosynthetic protein FliR
+Macromolecule #5: Flagellar biosynthetic protein FliP
+Macromolecule #6: Flagellar hook-basal body complex protein FliE
+Macromolecule #7: Flagellar basal body rod protein FlgB
+Macromolecule #8: Flagellar basal-body rod protein FlgC
+Macromolecule #9: Flagellar M-ring protein
+Macromolecule #10: Flagellar basal-body rod protein FlgF
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: SerialEM |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: in silico model / Details: Model-Angelo |
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Software | Name: UCSF Chimera (ver. 1.17) |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8wlq: |