8IBN | pdb_00008ibn

Cryo-EM structure of KpFtsZ single filament

PDB DOI: https://doi.org/10.2210/pdb8IBN/pdb
EM Map EMD-35344: EMDB EMDataResource

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

Deposited: 2023-02-10 Released: 2023-08-02
Deposition Author(s): Fujita, J., Amesaka, H., Yoshizawa, T., Kuroda, N., Kamimura, N., Hibino, K., Konishi, T., Kato, Y., Hara, M., Inoue, T., Namba, K., Tanaka, S., Matsumura, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Other private, Japan Science and Technology, Japan Agency for Medical Research and Development (AMED), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.03 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 164.54 kDa
Atom Count: 8,940
Modeled Residue Count: 1,224
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein FtsZ	A, B, C, D	385	Klebsiella pneumoniae	Mutation(s): 0
UniProt
Find proteins for W9BCK7 (Klebsiella pneumoniae) Explore W9BCK7 Go to UniProtKB: W9BCK7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W9BCK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G2P (Subject of Investigation/LOI) Query on G2P Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.03 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.1
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K05445
Japan Society for the Promotion of Science (JSPS)	Japan	JP21K05386
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06094
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H04735
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K22630
Other private	Japan	2018-3011
Other private	Japan	2022-4052
Japan Science and Technology	Japan	JPMJOP1861
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101117
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121003
Japan Agency for Medical Research and Development (AMED)	Japan	JP17pc0101020
Japan Agency for Medical Research and Development (AMED)		JP21am0101070
Other private		--
Other private		--
Other government		CR-20-02
Other government		CR-21-02