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- EMDB-2815: FtsAZ constriction in a liposome -

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Basic information

Entry
Database: EMDB / ID: EMD-2815
TitleFtsAZ constriction in a liposome
Map dataTomogram of the FtsZ ring reconstituted in liposomes.
Sample
  • Sample: Thermotoga maritima FtsA and FtsZ proteins encapsulated inside liposomes.
  • Protein or peptide: FtsZ
  • Protein or peptide: FtsA
KeywordsFtsZ / divisome / bacterial cell division / cytokinesis
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / cytoplasmic side of plasma membrane / cell division / GTPase activity / GTP binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Cell division protein FtsA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / Tubulin-like protein FtsZ/CetZ / 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. ...Cell division protein FtsA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / Tubulin-like protein FtsZ/CetZ / 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. / FtsZ protein signature 2. / 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Cell division protein FtsZ / Cell division protein FtsA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Methodelectron tomography / cryo EM
AuthorsSzwedziak P / Wang Q / Bharat TAM / Tsim M / Lowe J
CitationJournal: Elife / Year: 2014
Title: Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division.
Authors: Piotr Szwedziak / Qing Wang / Tanmay A M Bharat / Matthew Tsim / Jan Löwe /
Abstract: Membrane constriction is a prerequisite for cell division. The most common membrane constriction system in prokaryotes is based on the tubulin homologue FtsZ, whose filaments in E. coli are anchored ...Membrane constriction is a prerequisite for cell division. The most common membrane constriction system in prokaryotes is based on the tubulin homologue FtsZ, whose filaments in E. coli are anchored to the membrane by FtsA and enable the formation of the Z-ring and divisome. The precise architecture of the FtsZ ring has remained enigmatic. In this study, we report three-dimensional arrangements of FtsZ and FtsA filaments in C. crescentus and E. coli cells and inside constricting liposomes by means of electron cryomicroscopy and cryotomography. In vivo and in vitro, the Z-ring is composed of a small, single-layered band of filaments parallel to the membrane, creating a continuous ring through lateral filament contacts. Visualisation of the in vitro reconstituted constrictions as well as a complete tracing of the helical paths of the filaments with a molecular model favour a mechanism of FtsZ-based membrane constriction that is likely to be accompanied by filament sliding.
History
DepositionNov 7, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseDec 31, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.66
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2815.png

Downloads & links

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Map

FileDownload / File: emd_2815.map.gz / Format: CCP4 / Size: 10.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of the FtsZ ring reconstituted in liposomes.
Voxel sizeX=Y=Z: 17.98 Å
Density
Contour LevelBy EMDB: 2.66 / Movie #1: 2.66
Minimum - Maximum0.0 - 4.19936943
Average (Standard dev.)1.04198217 (±1.20530427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-412-464233
Dimensions16320285
Spacing16320285
CellA: 3631.96 Å / B: 2930.74 Å / C: 1528.2999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z17.9817.9817.98
M x/y/z20216385
origin x/y/z0.0000.0000.000
length x/y/z3631.9602930.7401528.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-464-412233
NC/NR/NS20216385
D min/max/mean0.0004.1991.042

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Supplemental data

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Sample components

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Entire : Thermotoga maritima FtsA and FtsZ proteins encapsulated inside li...

EntireName: Thermotoga maritima FtsA and FtsZ proteins encapsulated inside liposomes.
Components
  • Sample: Thermotoga maritima FtsA and FtsZ proteins encapsulated inside liposomes.
  • Protein or peptide: FtsZ
  • Protein or peptide: FtsA

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Supramolecule #1000: Thermotoga maritima FtsA and FtsZ proteins encapsulated inside li...

SupramoleculeName: Thermotoga maritima FtsA and FtsZ proteins encapsulated inside liposomes.
type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: FtsZ

MacromoleculeName: FtsZ / type: protein_or_peptide / ID: 1 / Oligomeric state: polymer / Recombinant expression: Yes
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 38 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C41 / Recombinant plasmid: pTXB1
SequenceUniProtKB: Cell division protein FtsZ

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Macromolecule #2: FtsA

MacromoleculeName: FtsA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: polymer / Recombinant expression: Yes
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 47 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C41 / Recombinant plasmid: pTXB1
SequenceUniProtKB: Cell division protein FtsA

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris 100 mM NaCl 1 mM EDTA 1 mM NaN3
GridDetails: Quantifoil R2/2 200 mesh Cu/Rh holey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: 3.5 s blot on Whatmann 1 filter paper.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 26000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -10.0 µm / Nominal defocus min: -10.0 µm / Nominal magnification: 26000
Specialist opticsEnergy filter - Name: Gatan Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1 °
Alignment procedureLegacy - Astigmatism: Visualisation of power spectrum.
DateAug 29, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 121 / Average electron dose: 150 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD, tomo3D / Number images used: 121
DetailsTilt series data was aligned using IMOD and reconstruction was carried out using tomo3D.

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