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- EMDB-1911: Tetrameric assembly intermediate of FtsZ1 from Arabidopsis thaliana -

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Basic information

Entry
Database: EMDB / ID: EMD-1911
TitleTetrameric assembly intermediate of FtsZ1 from Arabidopsis thaliana
Map dataThis is a tetrameric intermediate of Arabidopsis thaliana FtsZ1 assembly
Sample
  • Sample: Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1
  • Protein or peptide: Chloroplast
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: 0.844
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.844
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

EMD-1911.png

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Map

FileDownload / File: emd_1911.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a tetrameric intermediate of Arabidopsis thaliana FtsZ1 assembly
Voxel sizeX=Y=Z: 5.1 Å
Density
Contour LevelBy AUTHOR: 0.844 / Movie #1: 0.844
Minimum - Maximum-0.82676119 - 1.31319165
Average (Standard dev.)0.0 (±0.26896936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-5-5-5
Dimensions484848
Spacing484848
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-5-5-5
NC/NR/NS484848
D min/max/mean-0.8271.3130.000

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Supplemental data

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Sample components

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Entire : Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1

EntireName: Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1
Components
  • Sample: Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1
  • Protein or peptide: Chloroplast

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Supramolecule #1000: Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1

SupramoleculeName: Tetrameric assembly intermediate from Arabidopsis thaliana FtsZ1
type: sample / ID: 1000 / Oligomeric state: One homotetramer / Number unique components: 1
Molecular weightExperimental: 166 KDa / Theoretical: 166 KDa / Method: Native PAGE

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Macromolecule #1: Chloroplast

MacromoleculeName: Chloroplast / type: protein_or_peptide / ID: 1 / Name.synonym: Chloroplast / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Arabidopsis thaliana (thale cress) / synonym: Thale Cress / Organelle: Chloroplast
Molecular weightExperimental: 166 KDa / Theoretical: 166 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 Mg Acetate, 2 mM GTP
StainingType: NEGATIVE / Details: Negatively stained with 2% w/v uranyl acetate
GridDetails: 400 mesh copper
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1200EX
DateAug 11, 2010
Image recordingCategory: CCD / Film or detector model: SIA 15C (3k x 3k) / Number real images: 25 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: standard / Specimen holder model: JEOL

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Image processing

Detailsautoboxed
Final reconstructionApplied symmetry - Point group: C4 (4 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: 8000
Final two d classificationNumber classes: 20

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