8GZW | pdb_00008gzw

Klebsiella pneumoniae FtsZ complexed with monobody (P21)

• PDB DOI: https://doi.org/10.2210/pdb8GZW/pdb

• Classification: CELL CYCLE
• Organism(s): Klebsiella pneumoniae, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2023-07-19 
• Deposition Author(s): Matsumura, H., Yoshizawa, T., Fujita, J., Tanaka, S., Amesaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structures of a FtsZ single protofilament and a double-helical tube in complex with a monobody.

Fujita, J., Amesaka, H., Yoshizawa, T., Hibino, K., Kamimura, N., Kuroda, N., Konishi, T., Kato, Y., Hara, M., Inoue, T., Namba, K., Tanaka, S.I., Matsumura, H.

(2023) Nat Commun 14: 4073-4073

• PubMed: 37429870 
• DOI: https://doi.org/10.1038/s41467-023-39807-5
• Primary Citation Related Structures: 
  8GZV, 8GZW, 8GZX, 8GZY, 8H1O, 8IBN


• PubMed 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 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.

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Organizational Affiliation: 
• Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Graduate School of Life and Environmental Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan.
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan.
Open and Transdisciplinary Research Initiatives, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
dotAqua Inc., 2-1 Yamadaoka, Suita, Osaka, Japan.
RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Graduate School of Life and Environmental Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan. [e-mail].
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 126.11 kDa 
• Atom Count: 8,808 
• Modeled Residue Count: 1,193 
• Deposited Residue Count: 1,203 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein FtsZ	A, C, E	309	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ftsZ
UniProt
Find proteins for A0A0H3GRR0 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GRR0  Go to UniProtKB:  A0A0H3GRR0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody	B, D, F	92	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	G [auth A], H [auth C], I [auth E]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.471	α = 90
b = 66.933	β = 92.055
c = 102.172	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Matsumura, H., Yoshizawa, T., Fujita, J., Tanaka, S., Amesaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06094

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary