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Yorodumi- PDB-7sgo: Crystal structure of periplasmic domain of Helicobacter pylori Fl... -
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-Basic information
Entry | Database: PDB / ID: 7sgo | ||||||
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Title | Crystal structure of periplasmic domain of Helicobacter pylori FliL (residues 81 to 183) (crystal form B) | ||||||
Components | Flagellar protein FliL | ||||||
Keywords | MOTOR PROTEIN / Flagellar motor / FliL | ||||||
Function / homology | Flagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane / Flagellar protein FliL Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å | ||||||
Authors | Chan, K.L. / Peterson, B. / Khan, M.F. / Roujeinikova, A. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation. Authors: Shoichi Tachiyama / Kar L Chan / Xiaolin Liu / Skander Hathroubi / Briana Peterson / Mohammad F Khan / Karen M Ottemann / Jun Liu / Anna Roujeinikova / Abstract: The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and ...The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and activation remains largely enigmatic. Here, we show that one such assembly factor, the conserved protein FliL, forms an integral part of the flagellar motor in a position that colocalizes with the stator. Cryogenic electron tomography reconstructions of the intact motor in whole wild-type cells and cells lacking FliL revealed that the periplasmic domain of FliL (FliL-C) forms 18 circumferentially positioned rings integrated with the 18 MotAB units. FliL-C formed partial rings in the crystal, and the crystal structure-based full ring model was consistent with the shape of the rings observed in situ. Our data suggest that each FliL ring is coaxially sandwiched between the MotA ring and the dimeric periplasmic MotB moiety of the stator unit and that the central hole of the FliL ring has density that is consistent with the plug/linker region of MotB in its extended, active conformation. Significant structural similarities were found between FliL-C and stomatin/prohibitin/flotillin/HflK/C domains of scaffolding proteins, suggesting that FliL acts as a scaffold. The binding energy released upon association of FliL with the stator units could be used to power the release of the plug helices. The finding that isolated FliL-C forms stable partial rings provides an insight into the putative mechanism by which the FliL rings assemble around the stator units. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sgo.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sgo.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sgo_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 7sgo_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 7sgo_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7sgo_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sgo ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sgo | HTTPS FTP |
-Related structure data
Related structure data | 7sgnC 7sgpC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 12684.601 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fliL, BGL67_04255 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A293T1P9 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium di-hydrogen phosphate, trisodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→46.784 Å / Num. obs: 25074 / % possible obs: 93 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.69→2.83 Å / Rmerge(I) obs: 0.336 / Num. unique obs: 3405 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.695→46.784 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.02 Å2 / Biso mean: 41.9475 Å2 / Biso min: 11.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.695→46.784 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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