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- PDB-8gzw: Klebsiella pneumoniae FtsZ complexed with monobody (P21) -

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Basic information

Entry
Database: PDB / ID: 8gzw
TitleKlebsiella pneumoniae FtsZ complexed with monobody (P21)
Components
  • Cell division protein FtsZ
  • Monobody
KeywordsCELL 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
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
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMatsumura, H. / Yoshizawa, T. / Fujita, J. / Tanaka, S. / Amesaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18K06094 Japan
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
DepositionSep 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,1159
Polymers124,7856
Non-polymers1,3303
Water72140
1
A: Cell division protein FtsZ
B: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0383
Polymers41,5952
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-7 kcal/mol
Surface area16900 Å2
MethodPISA
2
C: Cell division protein FtsZ
D: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0383
Polymers41,5952
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-6 kcal/mol
Surface area16810 Å2
MethodPISA
3
E: Cell division protein FtsZ
F: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0383
Polymers41,5952
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-8 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.471, 66.933, 102.172
Angle α, β, γ (deg.)90.000, 92.055, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cell division protein FtsZ / / Filamenting temperature-sensitive mutant Z


Mass: 31813.107 Da / Num. of mol.: 3
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
#2: Antibody Monobody /


Mass: 9781.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M sodium formate, 0.1M Bis-Tris propane pH6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→40.05 Å / Num. obs: 41534 / % possible obs: 99.69 % / Redundancy: 6.9 % / Biso Wilson estimate: 55.89 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.57
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 4148 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LL5

6ll5


Resolution: 2.5→40.05 Å / SU ML: 0.4442 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.3394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2836 2076 5 %
Rwork0.2147 39453 -
obs0.2182 41529 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8684 0 84 40 8808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818885
X-RAY DIFFRACTIONf_angle_d1.07212074
X-RAY DIFFRACTIONf_chiral_restr0.06061445
X-RAY DIFFRACTIONf_plane_restr0.00811567
X-RAY DIFFRACTIONf_dihedral_angle_d11.66251306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.44281380.3422626X-RAY DIFFRACTION99.89
2.56-2.620.38711360.30612590X-RAY DIFFRACTION99.71
2.62-2.690.34821380.2742618X-RAY DIFFRACTION99.78
2.69-2.770.34861390.2692638X-RAY DIFFRACTION99.86
2.77-2.860.36091360.25592596X-RAY DIFFRACTION99.78
2.86-2.960.33951370.26872590X-RAY DIFFRACTION99.82
2.96-3.080.36061390.27432646X-RAY DIFFRACTION99.93
3.08-3.220.28781370.2512606X-RAY DIFFRACTION99.89
3.22-3.390.33681390.24012646X-RAY DIFFRACTION99.71
3.39-3.60.28621370.23262600X-RAY DIFFRACTION99.56
3.61-3.880.31271380.22552622X-RAY DIFFRACTION99.67
3.88-4.270.26981400.20262660X-RAY DIFFRACTION99.79
4.27-4.890.25951390.17792644X-RAY DIFFRACTION99.64
4.89-6.160.25271400.19162652X-RAY DIFFRACTION99.68
6.16-40.050.19841430.15692719X-RAY DIFFRACTION99.1

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