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Yorodumi- PDB-9iwq: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9iwq | ||||||
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Title | Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament | ||||||
Components | Flagellin | ||||||
Keywords | MOTOR PROTEIN / flagellin / tail / flagella / filament | ||||||
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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.08 Å | ||||||
Authors | Waraich, K. / Makino, F. / Miyata, T. / Kinoshita, M. / Minamino, T. / Namba, K. | ||||||
Funding support | Japan, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9iwq.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9iwq.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 9iwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9iwq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9iwq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9iwq_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 9iwq_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/9iwq ftp://data.pdbj.org/pub/pdb/validation_reports/iw/9iwq | HTTPS FTP |
-Related structure data
Related structure data | 60959MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42587.551 Da / Num. of mol.: 1 / Mutation: G426A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Gene: fliC, flaF, hag, STM1959 Production host: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) References: UniProt: P06179 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
-Processing
EM software |
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Image processing | Details: Helical processing using cryosparc. | ||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Helical symmerty | Angular rotation/subunit: 4.801 ° / Axial rise/subunit: 65.305 Å / Axial symmetry: C1 | ||||||||||||
Particle selection | Num. of particles selected: 726742 | ||||||||||||
3D reconstruction | Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 726742 / Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||
Atomic model building | PDB-ID: 3A5X Accession code: 3A5X / Details: 3A5X / Source name: PDB / Type: experimental model |