+Open data
-Basic information
Entry | Database: PDB / ID: 1ucu | ||||||
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Title | R-type straight flagellar filament made of full-length flagellin | ||||||
Components | phase 1 Flagellin | ||||||
Keywords | STRUCTURAL PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION | ||||||
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 typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Yonekura, K. / Maki-Yonekura, S. / Namba, K. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Authors: Koji Yonekura / Saori Maki-Yonekura / Keiichi Namba / Abstract: The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in ...The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling. The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization. Here we report a complete atomic model of the R-type filament by electron cryomicroscopy. A density map obtained from image data up to 4 A resolution shows the feature of alpha-helical backbone and some large side chains. The atomic model built on the map reveals intricate molecular packing and an alpha-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament. #1: Journal: NATURE / Year: 2001 Title: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling Authors: Samatey, F.A. / Imada, K. / Nagashima, S. / Vonderviszt, F. / Kumasaka, T. / Yamamoto, M. / Namba, K. | ||||||
History |
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Remark 244 | OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, ... OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, L01) : ( -5, 31) SELECTION RULE : L = 66 N + 361 M MAXIMUM BESSEL ORDER : 170 NUMBER OF LAYER-LINES : 298 NUMBER OF FILAMENT IMAGES : 102 NUMBER OF MOLECULAR IMAGES : 41,469 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 ALONG THE MERIDIAN EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 ALONG THE EQUATOR | ||||||
Remark 650 | HELIX Determination method: Author determined | ||||||
Remark 700 | SHEET Determination method: Author determined |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1ucu.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucu.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ucu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ucu_validation.pdf.gz | 363.2 KB | Display | wwPDB validaton report |
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Full document | 1ucu_full_validation.pdf.gz | 384.6 KB | Display | |
Data in XML | 1ucu_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1ucu_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucu ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 51551.203 Da / Num. of mol.: 1 / Mutation: A449V / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Strain: SJW 1665 / 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: R-TYPE STRAIGHT FLAGELLAR FILAMENT / Type: COMPLEX |
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Buffer solution | Name: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL / pH: 7.8 Details: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: QUANTIFOIL R1.2/1.3 (25 NM THICK) |
Crystal grow | *PLUS Method: unknown |
-Electron microscopy imaging
Microscopy | Model: JEOL 3000SFF |
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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: 50000 X / Calibrated magnification: 47600 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 1.6 mm |
Specimen holder | Temperature: 4 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
Software |
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EM software | Name: X-PLOR / Category: model fitting | ||||||||||||
CTF correction | Details: BOTH AMPLITUDE AND PHASE | ||||||||||||
3D reconstruction | Method: HELICAL RECONSTRUCTION / Resolution: 4 Å / Num. of particles: 102 / Nominal pixel size: 1 Å / Actual pixel size: 1.05 Å Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin ...Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated. Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: amplitude-weighted phase residual Details: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING | ||||||||||||
Atomic model building | PDB-ID: 1IO1 Accession code: 1IO1 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Resolution: 4→30 Å / Rfactor Rwork: 0.3 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→30 Å
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