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- PDB-9iue: cryo-EM structure of FtsE/X and ZipA complex in filament -

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Basic information

Entry
Database: PDB / ID: 9iue
Titlecryo-EM structure of FtsE/X and ZipA complex in filament
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
  • Cell division protein ZipA
KeywordsCELL CYCLE / cell division / division filament / FtsE/X / ZipA
Function / homology
Function and homology information


division septum / divisome complex / Gram-negative-bacterium-type cell wall / signal recognition particle binding / peptidoglycan turnover / plasma membrane protein complex / SRP-dependent cotranslational protein targeting to membrane / division septum assembly / FtsZ-dependent cytokinesis / cell division site ...division septum / divisome complex / Gram-negative-bacterium-type cell wall / signal recognition particle binding / peptidoglycan turnover / plasma membrane protein complex / SRP-dependent cotranslational protein targeting to membrane / division septum assembly / FtsZ-dependent cytokinesis / cell division site / ATPase complex / positive regulation of cell division / cell division / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain ...ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / Signal-recognition particle receptor FtsY / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cell division protein FtsX / Cell division protein ZipA / Cell division ATP-binding protein FtsE
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhu, K.F. / Li, J.W. / Luo, M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: To Be Published
Title: cryo-EM structure of FtsE/X and ZipA complex in filament
Authors: Zhu, K.F. / Li, J.W. / Luo, M.
History
DepositionJul 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Cell division protein ZipA
2: Cell division protein ZipA
5: Cell division ATP-binding protein FtsE
6: Cell division ATP-binding protein FtsE
A: Cell division protein FtsX
B: Cell division protein FtsX
C: Cell division protein FtsX
D: Cell division protein FtsX
E: Cell division protein ZipA
F: Cell division protein ZipA
G: Cell division ATP-binding protein FtsE
H: Cell division ATP-binding protein FtsE
I: Cell division protein FtsX
J: Cell division protein FtsX
K: Cell division protein ZipA
L: Cell division protein ZipA
M: Cell division ATP-binding protein FtsE
N: Cell division ATP-binding protein FtsE
O: Cell division protein FtsX
P: Cell division protein FtsX
Q: Cell division protein ZipA
R: Cell division protein ZipA
S: Cell division ATP-binding protein FtsE
T: Cell division ATP-binding protein FtsE
U: Cell division protein FtsX
V: Cell division protein FtsX
W: Cell division protein ZipA
X: Cell division protein ZipA
Y: Cell division ATP-binding protein FtsE
Z: Cell division ATP-binding protein FtsE
a: Cell division protein FtsX
b: Cell division protein FtsX
c: Cell division protein ZipA
d: Cell division protein ZipA
e: Cell division ATP-binding protein FtsE
f: Cell division ATP-binding protein FtsE
g: Cell division protein FtsX
h: Cell division protein FtsX
i: Cell division protein ZipA
j: Cell division protein ZipA
k: Cell division ATP-binding protein FtsE
l: Cell division ATP-binding protein FtsE
m: Cell division protein FtsX
n: Cell division protein FtsX
o: Cell division protein ZipA
p: Cell division protein ZipA
q: Cell division ATP-binding protein FtsE
r: Cell division ATP-binding protein FtsE
s: Cell division protein FtsX
t: Cell division protein FtsX
u: Cell division protein ZipA
v: Cell division protein ZipA
w: Cell division ATP-binding protein FtsE
x: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,808,22072
Polymers1,798,80154
Non-polymers9,41818
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cell division protein ZipA / FtsZ interacting protein A


Mass: 36517.199 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: zipA, b2412, JW2404 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P77173
#2: Protein
Cell division ATP-binding protein FtsE


Mass: 24832.695 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: ftsE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W1F1D8
#3: Protein
Cell division protein FtsX


Mass: 38583.500 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: ftsX, ftsS, b3462, JW3427 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC30
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*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: complex of FtsE/X-ZipA in filament / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1140GATAN K2 SUMMIT (4k x 4k)
2136.65GATAN K2 SUMMIT (4k x 4k)
3136.65GATAN K2 SUMMIT (4k x 4k)

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Processing

Image processing
IDImage recording-ID
11
22
33
41
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
44PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.3FSC 0.143 CUT-OFF19873619IUEPOINT
23.3FSC 0.143 CUT-OFF19421519IUEPOINT
33.3FSC 0.143 CUT-OFF19421519IUEPOINT
43.3FSC 0.143 CUT-OFF19421519IUEPOINT
53.3FSC 0.143 CUT-OFF19421519IUEPOINT
63.3FSC 0.143 CUT-OFF19421519IUEPOINT
73.3FSC 0.143 CUT-OFF19421519IUEPOINT
83.3FSC 0.143 CUT-OFF19421519IUEPOINT
93.3FSC 0.143 CUT-OFF19421519IUEPOINT
103.3FSC 0.143 CUT-OFF19421519IUEPOINT
113.3FSC 0.143 CUT-OFF19421519IUEPOINT
123.3FSC 0.143 CUT-OFF19421519IUEPOINT
133.3FSC 0.143 CUT-OFF19421519IUEPOINT
143.3FSC 0.143 CUT-OFF19421519IUEPOINT
153.3FSC 0.143 CUT-OFF19421519IUEPOINT
163.3FSC 0.143 CUT-OFF19421519IUEPOINT
173.3FSC 0.143 CUT-OFF19873629IUEPOINT
183.3FSC 0.143 CUT-OFF19421529IUEPOINT
193.3FSC 0.143 CUT-OFF19421529IUEPOINT
203.3FSC 0.143 CUT-OFF19421529IUEPOINT
213.3FSC 0.143 CUT-OFF19421529IUEPOINT
223.3FSC 0.143 CUT-OFF19421529IUEPOINT
233.3FSC 0.143 CUT-OFF19421529IUEPOINT
243.3FSC 0.143 CUT-OFF19421529IUEPOINT
253.3FSC 0.143 CUT-OFF19421529IUEPOINT
263.3FSC 0.143 CUT-OFF19421529IUEPOINT
273.3FSC 0.143 CUT-OFF19421529IUEPOINT
283.3FSC 0.143 CUT-OFF19421529IUEPOINT
293.3FSC 0.143 CUT-OFF19421529IUEPOINT
303.3FSC 0.143 CUT-OFF19421529IUEPOINT
313.3FSC 0.143 CUT-OFF19421529IUEPOINT
323.3FSC 0.143 CUT-OFF19421529IUEPOINT
333.3FSC 0.143 CUT-OFF19873639IUEPOINT
343.3FSC 0.143 CUT-OFF19421539IUEPOINT
353.3FSC 0.143 CUT-OFF19421539IUEPOINT
363.3FSC 0.143 CUT-OFF19421539IUEPOINT
373.3FSC 0.143 CUT-OFF19421539IUEPOINT
383.3FSC 0.143 CUT-OFF19421539IUEPOINT
393.3FSC 0.143 CUT-OFF19421539IUEPOINT
403.3FSC 0.143 CUT-OFF19421539IUEPOINT
413.3FSC 0.143 CUT-OFF19421539IUEPOINT
423.3FSC 0.143 CUT-OFF19421539IUEPOINT
433.3FSC 0.143 CUT-OFF19421539IUEPOINT
443.3FSC 0.143 CUT-OFF19421539IUEPOINT
453.3FSC 0.143 CUT-OFF19421539IUEPOINT
463.3FSC 0.143 CUT-OFF19421539IUEPOINT
473.3FSC 0.143 CUT-OFF19421539IUEPOINT
483.3FSC 0.143 CUT-OFF19421539IUEPOINT
493.3FSC 0.143 CUT-OFF19873649IUEPOINT
503.3FSC 0.143 CUT-OFF19421549IUEPOINT
513.3FSC 0.143 CUT-OFF19421549IUEPOINT
523.3FSC 0.143 CUT-OFF19421549IUEPOINT
533.3FSC 0.143 CUT-OFF19421549IUEPOINT
543.3FSC 0.143 CUT-OFF19421549IUEPOINT
553.3FSC 0.143 CUT-OFF19421549IUEPOINT
563.3FSC 0.143 CUT-OFF19421549IUEPOINT
573.3FSC 0.143 CUT-OFF19421549IUEPOINT
583.3FSC 0.143 CUT-OFF19421549IUEPOINT
593.3FSC 0.143 CUT-OFF19421549IUEPOINT
603.3FSC 0.143 CUT-OFF19421549IUEPOINT
613.3FSC 0.143 CUT-OFF19421549IUEPOINT
623.3FSC 0.143 CUT-OFF19421549IUEPOINT
633.3FSC 0.143 CUT-OFF19421549IUEPOINT
643.3FSC 0.143 CUT-OFF19421549IUEPOINT
RefinementHighest resolution: 3.3 Å

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