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- EMDB-35344: Cryo-EM structure of KpFtsZ single filament -

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Basic information

Entry
Database: EMDB / ID: EMD-35344
TitleCryo-EM structure of KpFtsZ single filament
Map data
Sample
  • Complex: Cryo-EM structure of KpFtsZ single filament
    • Complex: KpFtsZ
      • Protein or peptide: Cell division protein FtsZ
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: POTASSIUM ION
Keywordsbacterial cell division / divisome / monobody / CELL CYCLE
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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-like protein FtsZ/CetZ / 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
Cell division protein FtsZ
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Methodhelical 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, 16 items
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, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35344.png

Downloads & links

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Map

FileDownload / File: emd_35344.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 310.32 Å		1.03 Å/pix.
x 300 pix.
= 310.32 Å		1.03 Å/pix.
x 300 pix.
= 310.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0344 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4516435 - 1.0799681
Average (Standard dev.)-0.00021667841 (±0.01936063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 310.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35344_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35344_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35344_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of KpFtsZ single filament

EntireName: Cryo-EM structure of KpFtsZ single filament
Components
  • Complex: Cryo-EM structure of KpFtsZ single filament
    • Complex: KpFtsZ
      • Protein or peptide: Cell division protein FtsZ
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: POTASSIUM ION

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Supramolecule #1: Cryo-EM structure of KpFtsZ single filament

SupramoleculeName: Cryo-EM structure of KpFtsZ single filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: KpFtsZ

SupramoleculeName: KpFtsZ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: Cell division protein FtsZ

MacromoleculeName: Cell division protein FtsZ / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 40.574926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMFEPMELT NDAVIKVIGV GGGGGNAVEH MVRERIEGVE FFAVNTDAQA LRKTAVGQTI QIGSGITKGL GAGANPEVGR NAADEDREA LRAALDGADM VFIAAGMGGG TGTGAAPVVA EVAKDLGILT VAVVTKPFNF EGKKRMAFAE QGITELSKHV D SLITIPND ...String:
GHMFEPMELT NDAVIKVIGV GGGGGNAVEH MVRERIEGVE FFAVNTDAQA LRKTAVGQTI QIGSGITKGL GAGANPEVGR NAADEDREA LRAALDGADM VFIAAGMGGG TGTGAAPVVA EVAKDLGILT VAVVTKPFNF EGKKRMAFAE QGITELSKHV D SLITIPND KLLKVLGRGI SLLDAFGAAN DVLKGAVQGI AELITRPGLM NVDFADVRTV MSEMGYAMMG SGVASGEDRA EE AAEMAIS SPLLEDIDLS GARGVLVNIT AGFDLRLDEF ETVGNTIRAF ASDNATVVIG TSLDPDMNDE LRVTVVATGI GMD KRPEIT LVTNKQVQQP VMDRYQQHGM SPLTQEQKPA AKVVNDNTPQ TAKEPDYLDI PAFLRKQAD

UniProtKB: Cell division protein FtsZ

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
15.0 mMHEPES2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid
100.0 mMKClpotassium chloride
10.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride

Details: 1 mM GMPCPP was supplemented.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.9 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.02 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.025 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 551739
Segment selectionNumber selected: 3695707 / Software - Name: cryoSPARC (ver. 4.1.1)
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ll5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

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

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