9ISJ | pdb_00009isj

Crystal structure of Klebsiella pneumoniae ZapA

• PDB DOI: https://doi.org/10.2210/pdb9ISJ/pdb

• Classification: CELL CYCLE
• Organism(s): Klebsiella variicola 342
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-18 Released: 2025-07-23 
• Deposition Author(s): Fujita, J., Hibino, K., Kagoshima, G., Kamimura, N., Kato, Y., Uehara, R., Namba, K., Uchihashi, T., Matsumura, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Uehara Memorial Foundation, Nagase Science and Technology, Novartis Foundation, G-7 Foundation, Japan Science and Technology, The Program for the R-GIRO Research from the Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, JEOL YOKOGUSHI Research Alliance Laboratories of Osaka University, The Cooperative Research Program of the Institute for Protein Research, Osaka University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.239 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.228 (DCC) 

Starting Model: experimental

Literature

Structural basis for the interaction between the bacterial cell division proteins FtsZ and ZapA.

Fujita, J., Kasai, K., Hibino, K., Kagoshima, G., Kamimura, N., Tobita, S., Kato, Y., Uehara, R., Namba, K., Uchihashi, T., Matsumura, H.

(2025) Nat Commun 16: 5985-5985

• PubMed: 40593603 
• DOI: https://doi.org/10.1038/s41467-025-60940-w
• Primary Citation of Related Structures:  
  9ISJ, 9ISK


• PubMed 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 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.

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Organizational Affiliation: 
• Graduate School of Frontier Biosciences, University of Osaka, Osaka, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, University of Osaka, Osaka, Japan.
Graduate School of Pharmaceutical Sciences, University of Osaka, Osaka, Japan.
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.
Department of Physics, Nagoya University, Nagoya, Japan.
Department of Physics, Nagoya University, Nagoya, Japan. [e-mail].
Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan. [e-mail].
Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan. [e-mail].
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.25 kDa 
• Atom Count: 1,845 
• Modeled Residue Count: 211 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein ZapA	A, B	109	Klebsiella variicola 342	Mutation(s): 0  Gene Names: zapA, KPK_0754
UniProt
Find proteins for B5XUC8 (Klebsiella pneumoniae (strain 342)) Explore B5XUC8  Go to UniProtKB:  B5XUC8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.239 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.228 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.173	α = 90
b = 54.173	β = 90
c = 330.044	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Fujita, J., Hibino, K., Kagoshima, G., Kamimura, N., Kato, Y., Uehara, R., Namba, K., Uchihashi, T., Matsumura, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K22630
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K06418
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K01994
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02277
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02270
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K18033
Uehara Memorial Foundation	Japan	--
Nagase Science and Technology	Japan	--
Novartis Foundation	Japan	--
G-7 Foundation	Japan	--
Japan Science and Technology	Japan	JPMJOP1861
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 University	Japan	CR-22-02
The Cooperative Research Program of the Institute for Protein Research, Osaka University	Japan	CR-23-02

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release