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- PDB-9wsd: Cryo-EM structure of Escherichia coli FtsZ Filaments -

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Basic information

Entry
Database: PDB / ID: 9wsd
TitleCryo-EM structure of Escherichia coli FtsZ Filaments
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Bacteria Cell Division
Function / homology
Function and homology information


divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
FtsZ protein signature 2. / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...FtsZ protein signature 2. / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLi, J. / Luo, M.
Funding support Singapore, China, 4items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)A-0008412-00-00 Singapore
Ministry of Education (MoE, China)2024yc_yxhwbs10002 China
Ministry of Education (MoE, China)2024NSCQ-KJFZMSX0229 China
Ministry of Education (MoE, China)CSTB2024YCJH-KYXM0095 China
CitationJournal: To Be Published
Title: FtsZ Filaments
Authors: Li, J. / Xu, X.
History
DepositionSep 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2208
Polymers161,4474
Non-polymers1,7734
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cell division protein FtsZ


Mass: 40361.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ftsZ, sfiB, sulB, b0095, JW0093
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A9A6
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FtsZ Filaments / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 6.02 sec. / Electron dose: 40.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117176 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048662
ELECTRON MICROSCOPYf_angle_d1.02111760
ELECTRON MICROSCOPYf_dihedral_angle_d4.6411298
ELECTRON MICROSCOPYf_chiral_restr0.0611434
ELECTRON MICROSCOPYf_plane_restr0.0051543

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