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- EMDB-34429: Cryo-EM structure of KpFtsZ-monobody double helical tube -

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Basic information

Entry
Database: EMDB / ID: EMD-34429
TitleCryo-EM structure of KpFtsZ-monobody double helical tube
Map data
Sample
  • Complex: Cryo-EM structure of KpFtsZ-monobody double helical tube
    • Complex: KpFtsZ
      • Protein or peptide: Cell division protein FtsZ
    • Complex: monobody
      • Protein or peptide: Mb(Ec/KpFtsZ_S1)
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
Keywordsbacterial cell division / divisome / FtsZ / monobody / tubulin / 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) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsFujita J / Amesaka H / Yoshizawa T / Kuroda N / Kamimura N / 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
the Japan Science Society2018-3011 Japan
the Japan Science Society2022-4052 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
JEOL YOKOGUSHI Research Alliance Laboratories of Osaka University Japan
Institute for Protein Research, Osaka UniversityCR-20-02 Japan
Institute for Protein Research, Osaka UniversityCR-21-02 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
G-7 Scholarship Foundation
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
DepositionOct 3, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34429.png

Downloads & links

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Map

FileDownload / File: emd_34429.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 600 pix.
= 529.8 Å		0.88 Å/pix.
x 600 pix.
= 529.8 Å		0.88 Å/pix.
x 600 pix.
= 529.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.883 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.49292547 - 1.086188
Average (Standard dev.)0.003854179 (±0.038149312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 529.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34429_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34429_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34429_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Cryo-EM structure of KpFtsZ-monobody double helical tube

EntireName: Cryo-EM structure of KpFtsZ-monobody double helical tube
Components
  • Complex: Cryo-EM structure of KpFtsZ-monobody double helical tube
    • Complex: KpFtsZ
      • Protein or peptide: Cell division protein FtsZ
    • Complex: monobody
      • Protein or peptide: Mb(Ec/KpFtsZ_S1)
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of KpFtsZ-monobody double helical tube

SupramoleculeName: Cryo-EM structure of KpFtsZ-monobody double helical tube
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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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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Supramolecule #3: monobody

SupramoleculeName: monobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cell division protein FtsZ

MacromoleculeName: Cell division protein FtsZ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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: Mb(Ec/KpFtsZ_S1)

MacromoleculeName: Mb(Ec/KpFtsZ_S1) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.781873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSVSSVPTKL EVVAATPTSL LISWDAPAVT VSYYRITYGE TGGNSPVQEF TVPGSKSTAT ISGLSPGVDY TITVYARSAY HRRSPISIN YRT

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid
100.0 mMKClpotassium chloride
25.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride

Details: 1 mM GMPPNP and 0.12 mM PC190723 were supplemented.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE
Details: The graphene grid was chemically oxidized and modified.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details1.2x molar excess of Mb was supplemented.

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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: 3.0 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: 7.703 Å
Applied symmetry - Helical parameters - Δ&Phi: -23.398 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 90711
Segment selectionNumber selected: 181247 / Software - Name: cryoSPARC (ver. 3.3.1)
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8h1o:
Cryo-EM structure of KpFtsZ-monobody double helical tube

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