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- EMDB-1910: Dimeric Homodimer of FtsZ1 from Arabidopsis thaliana -

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Basic information

Entry
Database: EMDB / ID: EMD-1910
TitleDimeric Homodimer of FtsZ1 from Arabidopsis thaliana
Map dataThis is a homodimer of FtsZ1 monomers from Arabidopsis thaliana.
Sample
  • Sample: Arabidopsis FtsZ1 homodimer
  • Protein or peptide: GTPase
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsSmith AG / Johnson CB / Vitha S / Holzenburg A
CitationJournal: Arch Biochem Biophys / Year: 2011
Title: Oligomerization of plant FtsZ1 and FtsZ2 plastid division proteins.
Authors: Aaron G Smith / Carol B Johnson / Stanislav Vitha / Andreas Holzenburg /
Abstract: FtsZ was identified in bacteria as the first protein to localize mid-cell prior to division and homologs have been found in many plant species. Bacterial studies demonstrated that FtsZ forms a ring ...FtsZ was identified in bacteria as the first protein to localize mid-cell prior to division and homologs have been found in many plant species. Bacterial studies demonstrated that FtsZ forms a ring structure that is dynamically exchanged with a soluble pool of FtsZ. Our previous work established that Arabidopsis FtsZ1 and FtsZ2-1 are capable of in vitro self-assembly into two distinct filament types, termed type-I and type-II and noted the presence of filament precursor molecules which prompted this investigation. Using a combination of electron microscopy, gel chromatography and native PAGE revealed that (i) prior to FtsZ assembly initiation the pool consists solely of dimers and (ii) during assembly of the Arabidopsis FtsZ type-II filaments the most common intermediate between the dimer and filament state is a tetramer. Three-dimensional reconstructions of the observed dimer and tetramer suggest these oligomeric forms may represent consecutive steps in type-II filament assembly and a mechanism is proposed, which is expanded to include FtsZ assembly into type-I filaments. Finally, the results permit a discussion of the oligomeric nature of the soluble pool in plants.
History
DepositionJun 21, 2011-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1910.png

Downloads & links

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Map

FileDownload / File: emd_1910.map.gz / Format: CCP4 / Size: 179.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a homodimer of FtsZ1 monomers from Arabidopsis thaliana.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 36 pix.
= 183.6 Å		5.1 Å/pix.
x 36 pix.
= 183.6 Å		5.1 Å/pix.
x 36 pix.
= 183.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.07 / Movie #1: 1.07
Minimum - Maximum-0.47544459 - 1.35954654
Average (Standard dev.)0.0 (±0.24924706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-18-18-18
Dimensions363636
Spacing363636
CellA=B=C: 183.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z363636
origin x/y/z0.0000.0000.000
length x/y/z183.600183.600183.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-18-18-18
NC/NR/NS363636
D min/max/mean-0.4751.360-0.000

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Supplemental data

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Sample components

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Entire : Arabidopsis FtsZ1 homodimer

EntireName: Arabidopsis FtsZ1 homodimer
Components
  • Sample: Arabidopsis FtsZ1 homodimer
  • Protein or peptide: GTPase

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Supramolecule #1000: Arabidopsis FtsZ1 homodimer

SupramoleculeName: Arabidopsis FtsZ1 homodimer / type: sample / ID: 1000 / Oligomeric state: Homodimer / Number unique components: 1
Molecular weightExperimental: 85 KDa / Theoretical: 85 KDa / Method: Gel chromatography

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Macromolecule #1: GTPase

MacromoleculeName: GTPase / type: protein_or_peptide / ID: 1 / Name.synonym: GTPase / Oligomeric state: Homodimer / Recombinant expression: Yes
Source (natural)Organism: Arabidopsis thaliana (thale cress) / synonym: Thale Cress / Organelle: Chloroplast
Molecular weightExperimental: 85 KDa / Theoretical: 85 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus) / Recombinant plasmid: pPICZ

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 6.5 / Details: 100 mM MES, 1 mM EGTA, 5 mM MgAc, 2 mM GTP
StainingType: NEGATIVE
Details: Negative staining using 2% w/v uranyl acetate, protein was adsorbed for 10-20 sec
GridDetails: 400 mesh copper
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1200EX
Alignment procedureLegacy - Astigmatism: Was corrected at 100kx
DateSep 21, 2010
Image recordingCategory: CCD / Film or detector model: SIA 15C (3k x 3k) / Number real images: 15 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Standard / Specimen holder model: JEOL

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Image processing

DetailsAutoboxing
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12000
Final two d classificationNumber classes: 20

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