8GZW | pdb_00008gzw

Klebsiella pneumoniae FtsZ complexed with monobody (P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.284 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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

  • DOI: https://doi.org/10.1038/s41467-023-39807-5
  • Primary Citation of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsZ
A, C, E
309Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ftsZ
UniProt
Find proteins for A0A0H3GRR0 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
Explore A0A0H3GRR0 
Go to UniProtKB:  A0A0H3GRR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3GRR0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monobody
B, D, F
92Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.471α = 90
b = 66.933β = 92.055
c = 102.172γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18K06094

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description