+Open data
-Basic information
Entry | Database: PDB / ID: 8h1o | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of KpFtsZ-monobody double helical tube | |||||||||||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | CELL CYCLE / bacterial cell division / divisome / FtsZ / monobody / tubulin | |||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Fujita, J. / Amesaka, H. / Yoshizawa, T. / Kuroda, N. / Kamimura, N. / Hara, M. / Inoue, T. / Namba, K. / Tanaka, S. / Matsumura, H. | |||||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 16items
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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 | 8h1o.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h1o.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/8h1o ftp://data.pdbj.org/pub/pdb/validation_reports/h1/8h1o | HTTPS FTP |
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-Related structure data
Related structure data | 34429MC 8gzvC 8gzwC 8gzxC 8gzyC 8ibnC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 40574.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W9BCK7 |
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#2: Protein | 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 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 Details: 1 mM GMPPNP and 0.12 mM PC190723 were supplemented. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 1.2x molar excess of Mb was supplemented. | |||||||||||||||||||||||||
Specimen support | Details: The graphene grid was chemically oxidized and modified. Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -23.398 ° / Axial rise/subunit: 7.703 Å / Axial symmetry: C2 | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 181247 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90711 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.49 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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