6UMK | pdb_00006umk

Structure of E. coli FtsZ(L178E)-GDP complex

  • Classification: CELL CYCLE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-10-09 Released: 2020-02-05 
  • Deposition Author(s): Schumacher, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP.

Schumacher, M.A.Ohashi, T.Corbin, L.Erickson, H.P.

(2020) Acta Crystallogr F Struct Biol Commun 76: 94-102

  • DOI: https://doi.org/10.1107/S2053230X20001132
  • Primary Citation Related Structures: 
    6UMK, 6UNX

  • PubMed Abstract: 

    Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Box 3711, DUMC, Durham, NC 27710, USA.

Macromolecule Content 

  • Total Structure Weight: 32.19 kDa 
  • Atom Count: 2,532 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division protein FtsZ308Escherichia coliMutation(s): 1 
Gene Names: ftsZD4U49_01465DNQ92_00675
UniProt
Find proteins for P0A9A6 (Escherichia coli (strain K12))
Explore P0A9A6 
Go to UniProtKB:  P0A9A6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9A6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.427α = 90
b = 85.189β = 106.92
c = 41.398γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130290

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description