8GZX | pdb_00008gzx

Escherichia coli FtsZ complexed with monobody (P212121)

• PDB DOI: https://doi.org/10.2210/pdb8GZX/pdb

• Classification: CELL CYCLE
• Organism(s): Escherichia coli, 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: 1.84 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.207 (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

Macromolecule Content 

• Total Structure Weight: 42.04 kDa 
• Atom Count: 3,021 
• Modeled Residue Count: 394 
• Deposited Residue Count: 401 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein FtsZ	A	309	Escherichia coli	Mutation(s): 0  Gene Names: ftsZ, DNQ45_06620
UniProt
Find proteins for P0A9A6 (Escherichia coli (strain K12)) Explore P0A9A6  Go to UniProtKB:  P0A9A6

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.105	α = 90
b = 63.301	β = 90
c = 123.049	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