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- PDB-9isj: Crystal structure of Klebsiella pneumoniae ZapA -

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Basic information

Entry
Database: PDB / ID: 9isj
TitleCrystal structure of Klebsiella pneumoniae ZapA
ComponentsCell division protein ZapA
KeywordsCELL CYCLE / Bacterial cell division
Function / homology
Function and homology information


septin ring assembly / cell septum / division septum assembly / FtsZ-dependent cytokinesis / cell division site / plasma membrane / cytosol
Similarity search - Function
Cell division protein ZapA, eubacteria / Cell division protein ZapA, N-terminal / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA
Similarity search - Domain/homology
Cell division protein ZapA
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFujita, J. / Hibino, K. / Kagoshima, G. / Kamimura, N. / Kato, Y. / Uehara, R. / Namba, K. / Uchihashi, T. / Matsumura, H.
Funding support Japan, 15items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20K22630 Japan
Japan Society for the Promotion of Science (JSPS)JP23K06418 Japan
Japan Society for the Promotion of Science (JSPS)JP24K01994 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02277 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02270 Japan
Japan Society for the Promotion of Science (JSPS)JP23K18033 Japan
Uehara Memorial Foundation Japan
Nagase Science and Technology Japan
Novartis Foundation Japan
G-7 Foundation Japan
Japan Science and TechnologyJPMJOP1861 Japan
The Program for the R-GIRO Research from the Ritsumeikan Global Innovation Research Organization, Ritsumeikan University Japan
JEOL YOKOGUSHI Research Alliance Laboratories of Osaka University Japan
The Cooperative Research Program of the Institute for Protein Research, Osaka UniversityCR-22-02 Japan
The Cooperative Research Program of the Institute for Protein Research, Osaka UniversityCR-23-02 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the interaction between the bacterial cell division proteins FtsZ and ZapA.
Authors: Junso Fujita / Kazuki Kasai / Kota Hibino / Gota Kagoshima / Natsuki Kamimura / Shungo Tobita / Yuki Kato / Ryo Uehara / Keiichi Namba / Takayuki Uchihashi / Hiroyoshi Matsumura /
Abstract: Cell division in most bacteria is regulated by the tubulin homolog FtsZ as well as ZapA, a FtsZ-associated protein. However, how FtsZ and ZapA function coordinately has remained elusive. Here we ...Cell division in most bacteria is regulated by the tubulin homolog FtsZ as well as ZapA, a FtsZ-associated protein. However, how FtsZ and ZapA function coordinately has remained elusive. Here we report the cryo-electron microscopy structure of the ZapA-FtsZ complex at 2.73 Å resolution. The complex forms an asymmetric ladder-like structure, in which the double antiparallel FtsZ protofilament on one side and a single protofilament on the other side are tethered by ZapA tetramers. In the complex, the extensive interactions of FtsZ with ZapA cause a structural change of the FtsZ protofilament, and the formation of the double FtsZ protofilament increases electrostatic repulsion. High-speed atomic force microscopy analysis revealed cooperative interactions of ZapA with FtsZ at a molecular level. Our findings not only provide a structural basis for the interaction between FtsZ and ZapA but also shed light on how ZapA binds to FtsZ protofilaments without disturbing FtsZ dynamics to promote cell division.
History
DepositionJul 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ZapA
B: Cell division protein ZapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2543
Polymers25,2182
Non-polymers351
Water2,378132
1
A: Cell division protein ZapA
B: Cell division protein ZapA
hetero molecules

A: Cell division protein ZapA
B: Cell division protein ZapA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5086
Polymers50,4374
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area15670 Å2
ΔGint-133 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.173, 54.173, 330.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cell division protein ZapA / Z ring-associated protein ZapA


Mass: 12609.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (strain 342) (bacteria)
Strain: 342 / Gene: zapA, KPK_0754 / Production host: Escherichia coli (E. coli) / References: UniProt: B5XUC8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium citrate pH5.5, and 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.45 Å / Num. obs: 28055 / % possible obs: 99.84 % / Redundancy: 9 % / CC1/2: 0.999 / Net I/σ(I): 20.03
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 2712 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.448 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2393 1361 4.852 %
Rwork0.2186 26691 -
all0.22 --
obs-28052 99.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20.004 Å2-0 Å2
2--0.008 Å2-0 Å2
3----0.025 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 1 132 1845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121727
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161575
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6542322
X-RAY DIFFRACTIONr_angle_other_deg0.8071.553698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3875208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.5761021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84910338
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8071099
X-RAY DIFFRACTIONr_chiral_restr0.0770.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022007
X-RAY DIFFRACTIONr_gen_planes_other0.010.02309
X-RAY DIFFRACTIONr_nbd_refined0.2240.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21345
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3370.230
X-RAY DIFFRACTIONr_nbd_other0.2640.2148
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.228
X-RAY DIFFRACTIONr_mcbond_it3.9114.083841
X-RAY DIFFRACTIONr_mcbond_other3.9044.082841
X-RAY DIFFRACTIONr_mcangle_it5.0776.0881046
X-RAY DIFFRACTIONr_mcangle_other5.0836.0951047
X-RAY DIFFRACTIONr_scbond_it5.8914.898886
X-RAY DIFFRACTIONr_scbond_other5.8474.896885
X-RAY DIFFRACTIONr_scangle_it8.6417.061276
X-RAY DIFFRACTIONr_scangle_other8.6387.0631277
X-RAY DIFFRACTIONr_lrange_it9.91978.9741952
X-RAY DIFFRACTIONr_lrange_other9.87574.7441920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.369910.34818960.34919870.8930.8981000.325
1.847-1.8970.315930.30618720.30719650.930.9291000.273
1.897-1.9520.325960.28318240.28519210.930.93999.94790.241
1.952-2.0120.273960.24717570.24918540.9540.95899.94610.21
2.012-2.0780.25960.2417280.2418250.960.9699.94520.205
2.078-2.1510.288860.23716330.2417220.9370.96499.82580.209
2.151-2.2320.369750.21516280.22117040.8990.9799.94130.187
2.232-2.3230.26780.21215540.21516320.9560.9711000.187
2.323-2.4260.302680.22215000.22515690.9380.9799.93630.194
2.426-2.5440.217820.21414340.21415170.9680.97299.93410.199
2.544-2.6810.231550.21114030.21214620.9640.97299.72640.195
2.681-2.8430.234690.21913080.21913820.9670.9799.63820.207
2.843-3.0380.247540.23112450.23112990.9540.9671000.231
3.038-3.2810.259730.2311360.23112090.9540.9681000.233
3.281-3.5920.239510.21911050.2211560.9670.9731000.229
3.592-4.0130.238540.2069740.20810280.9590.9771000.227
4.013-4.6280.172530.1748900.1749440.9830.98199.89410.211
4.628-5.6540.207420.1977650.1988090.9820.97999.75280.245
5.654-7.9370.266350.2546350.2556730.9540.96799.55420.309
7.937-46.4480.22140.2214040.2214290.9610.96497.43590.309

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