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Yorodumi- EMDB-60959: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60959 | |||||||||
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Title | Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament | |||||||||
Map data | ||||||||||
Sample |
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Keywords | flagellin / tail / flagella / filament / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / structural molecule activity / extracellular region Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.08 Å | |||||||||
Authors | Waraich K / Makino F / Miyata T / Kinoshita M / Minamino T / Namba K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: To Be Published Title: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament Authors: Waraich K / Makino F / Miyata T / Kinoshita M / Minamino T / Namba K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60959.map.gz | 37.8 MB | EMDB map data format | |
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Header (meta data) | emd-60959-v30.xml emd-60959.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60959_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_60959.png | 73.3 KB | ||
Filedesc metadata | emd-60959.cif.gz | 6.1 KB | ||
Others | emd_60959_half_map_1.map.gz emd_60959_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60959 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60959 | HTTPS FTP |
-Validation report
Summary document | emd_60959_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_60959_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_60959_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_60959_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60959 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60959 | HTTPS FTP |
-Related structure data
Related structure data | 9iwqMC 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_60959.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60959_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60959_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)...
Entire | Name: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament |
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Components |
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-Supramolecule #1: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)...
Supramolecule | Name: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament 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) |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Molecular weight | Theoretical: 42.587551 KDa |
Recombinant expression | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) |
Sequence | String: AQVINTNSLS LLTQNNLNKS QSALGTAIER LSSGLRINSA KDDAAGQAIA NRFTANIKGL TQASRNANDG ISIAQTTEGA LNEINNNLQ RVRELAVQSA NSTNSQSDLD SIQAEITQRL NEIDRVSGQT QFNGVKVLAQ DNTLTIQVGA NDGETIDIDL K QINSQTLG ...String: AQVINTNSLS LLTQNNLNKS QSALGTAIER LSSGLRINSA KDDAAGQAIA NRFTANIKGL TQASRNANDG ISIAQTTEGA LNEINNNLQ RVRELAVQSA NSTNSQSDLD SIQAEITQRL NEIDRVSGQT QFNGVKVLAQ DNTLTIQVGA NDGETIDIDL K QINSQTLG LDTLNVQQKY KVSDTAATVT GYADTTIALD NSTFKAALTA AGVTGTASVV KMSYTDNNGK TIDGGLAVKV GD DYYSATQ NKDGSISINT TKYTADDGTS KTALNKLGGA DGKTEVVSIG GKTYAASKAE GHNFKAQPDL AEAAATTTEN PLQ KIDAAL AQVDTLRSDL AAVQNRFNSA ITNLGNTVNN LTSARSRIED SDYATEVSNM SRAQILQQAG TSVLAQANQV PQNV LSLLR UniProtKB: Flagellin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 40.0 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: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |