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- PDB-8ibn: Cryo-EM structure of KpFtsZ single filament -

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Basic information

Entry
Database: PDB / ID: 8ibn
TitleCryo-EM structure of KpFtsZ single filament
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / bacterial cell division / divisome / monobody
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsFujita, J. / Amesaka, H. / Yoshizawa, T. / Kuroda, N. / Kamimura, N. / Hibino, K. / Konishi, T. / Kato, Y. / Hara, M. / Inoue, T. ...Fujita, J. / Amesaka, H. / Yoshizawa, T. / Kuroda, N. / Kamimura, N. / Hibino, K. / Konishi, T. / Kato, Y. / Hara, M. / Inoue, T. / Namba, K. / Tanaka, S. / Matsumura, H.
Funding support Japan, 16items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18K05445 Japan
Japan Society for the Promotion of Science (JSPS)JP21K05386 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06094 Japan
Japan Society for the Promotion of Science (JSPS)JP19H04735 Japan
Japan Society for the Promotion of Science (JSPS)JP20K22630 Japan
Other private2018-3011 Japan
Other private2022-4052 Japan
Japan Science and TechnologyJPMJOP1861 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101070
Other private
Other private
Other governmentCR-20-02
Other governmentCR-21-02
CitationJournal: 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
DepositionFeb 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,54112
Polymers162,3004
Non-polymers2,2418
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11510 Å2
ΔGint-71 kcal/mol
Surface area50120 Å2
MethodPISA

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Components

#1: Protein
Cell division protein FtsZ


Mass: 40574.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W9BCK7
#2: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of KpFtsZ single filamentCOMPLEX#10MULTIPLE SOURCES
2KpFtsZCOMPLEX#11RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 1 mM GMPCPP was supplemented.
Buffer component
IDConc.NameFormulaBuffer-ID
115 mM2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acidHEPES1
2100 mMpotassium chlorideKCl1
310 mMsodium chlorideNaCl1
45 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 2.9 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2SerialEM4image acquisition
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.15model fitting
9cryoSPARC4.1.1initial Euler assignment
10cryoSPARC4.1.1final Euler assignment
12cryoSPARC4.1.13D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.025 ° / Axial rise/subunit: 44.02 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 3695707
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 551739 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6LL5

6ll5


Accession code: 6LL5 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049028
ELECTRON MICROSCOPYf_angle_d0.82212236
ELECTRON MICROSCOPYf_dihedral_angle_d7.6271340
ELECTRON MICROSCOPYf_chiral_restr0.0551456
ELECTRON MICROSCOPYf_plane_restr0.0051608

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