+Open data
-Basic information
Entry | Database: PDB / ID: 8gzv | ||||||
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Title | Klebsiella pneumoniae FtsZ complexed with monobody (P212121) | ||||||
Components |
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Keywords | CELL CYCLE / Cell division / Monobody / GTPase / HYDROLASE | ||||||
Function / homology | Function and homology information FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Matsumura, H. / Yoshizawa, T. / Fujita, J. / Tanaka, S. / Amesaka, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody. Authors: Junso Fujita / Hiroshi Amesaka / Takuya Yoshizawa / Kota Hibino / Natsuki Kamimura / Natsuko Kuroda / Takamoto Konishi / Yuki Kato / Mizuho Hara / Tsuyoshi Inoue / Keiichi Namba / Shun-Ichi ...Authors: Junso Fujita / Hiroshi Amesaka / Takuya Yoshizawa / Kota Hibino / Natsuki Kamimura / Natsuko Kuroda / Takamoto Konishi / Yuki Kato / Mizuho Hara / Tsuyoshi Inoue / Keiichi Namba / Shun-Ichi Tanaka / Hiroyoshi Matsumura / Abstract: FtsZ polymerizes into protofilaments to form the Z-ring that acts as a scaffold for accessory proteins during cell division. Structures of FtsZ have been previously solved, but detailed mechanistic ...FtsZ polymerizes into protofilaments to form the Z-ring that acts as a scaffold for accessory proteins during cell division. Structures of FtsZ have been previously solved, but detailed mechanistic insights are lacking. Here, we determine the cryoEM structure of a single protofilament of FtsZ from Klebsiella pneumoniae (KpFtsZ) in a polymerization-preferred conformation. We also develop a monobody (Mb) that binds to KpFtsZ and FtsZ from Escherichia coli without affecting their GTPase activity. Crystal structures of the FtsZ-Mb complexes reveal the Mb binding mode, while addition of Mb in vivo inhibits cell division. A cryoEM structure of a double-helical tube of KpFtsZ-Mb at 2.7 Å resolution shows two parallel protofilaments. Our present study highlights the physiological roles of the conformational changes of FtsZ in treadmilling that regulate cell division. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gzv.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gzv.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/8gzv ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gzv | HTTPS FTP |
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-Related structure data
Related structure data | 8gzwC 8gzxC 8gzyC 8h1oC 8ibnC 6ll5S S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 31813.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ftsZ / Production host: Escherichia coli (E. coli) / References: UniProt: W9BCK7 |
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#2: Antibody | Mass: 9781.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M sodium formate, 0.1M Bis-Tris propane pH6.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35.54 Å / Num. obs: 19223 / % possible obs: 99.86 % / Redundancy: 13 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.67 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 1877 / CC1/2: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LL5 Resolution: 2.2→35.54 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.0416 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 46.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.54 Å
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Refine LS restraints |
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LS refinement shell |
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