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- EMDB-2505: Septin-Gic1 complex in a single-tilt-axis subtomogram. -

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Basic information

Entry
Database: EMDB / ID: EMD-2505
TitleSeptin-Gic1 complex in a single-tilt-axis subtomogram.
Map dataCryo-Tomogram of Septin/Gic1 Complex.
Sample
  • Sample: Septin-Gic1 complex
  • Protein or peptide: Septin
  • Protein or peptide: Gic1
Keywordscell division / bud neck filaments / cytokinesis / cytoskeleton / electron tomography / septin / gic
Function / homology
Function and homology information


septin ring organization / Cdc42 protein signal transduction / incipient cellular bud site / cellular bud tip / regulation of exit from mitosis / cellular bud neck / mating projection tip / establishment of cell polarity / small GTPase binding / regulation of cell shape ...septin ring organization / Cdc42 protein signal transduction / incipient cellular bud site / cellular bud tip / regulation of exit from mitosis / cellular bud neck / mating projection tip / establishment of cell polarity / small GTPase binding / regulation of cell shape / cell cortex / cytoskeleton / nucleus / cytoplasm
Similarity search - Function
Septin / CRIB domain profile. / P21-Rho-binding domain / CRIB domain
Similarity search - Domain/homology
GTPase-interacting component 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM / Resolution: 60.0 Å
AuthorsSadian Y / Gatsogiannis C / Patasi C / Hofnagel O / Goody RS / Farkasovsky M / Raunser S
CitationJournal: Elife / Year: 2013
Title: The role of Cdc42 and Gic1 in the regulation of septin filament formation and dissociation.
Authors: Yashar Sadian / Christos Gatsogiannis / Csilla Patasi / Oliver Hofnagel / Roger S Goody / Marian Farkasovský / Stefan Raunser /
Abstract: Septins are guanine nucleotide-binding proteins that polymerize into filamentous and higher-order structures. Cdc42 and its effector Gic1 are involved in septin recruitment, ring formation and ...Septins are guanine nucleotide-binding proteins that polymerize into filamentous and higher-order structures. Cdc42 and its effector Gic1 are involved in septin recruitment, ring formation and dissociation. The regulatory mechanisms behind these processes are not well understood. Here, we have used electron microscopy and cryo electron tomography to elucidate the structural basis of the Gic1-septin and Gic1-Cdc42-septin interaction. We show that Gic1 acts as a scaffolding protein for septin filaments forming long and flexible filament cables. Cdc42 in its GTP-form binds to Gic1, which ultimately leads to the dissociation of Gic1 from the filament cables. Surprisingly, Cdc42-GDP is not inactive, but in the absence of Gic1 directly interacts with septin filaments resulting in their disassembly. We suggest that this unanticipated dual function of Cdc42 is crucial for the cell cycle. Based on our results we propose a novel regulatory mechanism for septin filament formation and dissociation. DOI: http://dx.doi.org/10.7554/eLife.01085.001.
History
DepositionOct 27, 2013-
Header (metadata) releaseNov 6, 2013-
Map releaseDec 11, 2013-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2505.jpg

Downloads & links

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Map

FileDownload / File: emd_2505.map.gz / Format: CCP4 / Size: 6.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-Tomogram of Septin/Gic1 Complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 72 pix.
= 518.4 Å		7.2 Å/pix.
x 202 pix.
= 1454.4 Å		7.2 Å/pix.
x 126 pix.
= 907.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.2 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-12.639062880000001 - 8.68243599
Average (Standard dev.)-0.69266033 (±2.53066993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-116-286-2
Dimensions20212672
Spacing20212672
CellA: 907.19995 Å / B: 1454.3999 Å / C: 518.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z12620272
origin x/y/z0.0000.0000.000
length x/y/z907.2001454.400518.400
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-286-116-2
NC/NR/NS12620272
D min/max/mean-12.6398.682-0.693

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Supplemental data

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Sample components

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Entire : Septin-Gic1 complex

EntireName: Septin-Gic1 complex
Components
  • Sample: Septin-Gic1 complex
  • Protein or peptide: Septin
  • Protein or peptide: Gic1

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Supramolecule #1000: Septin-Gic1 complex

SupramoleculeName: Septin-Gic1 complex / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: Septin

MacromoleculeName: Septin / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FMY1027 / synonym: Yeast
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceInterPro: Septin

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Macromolecule #2: Gic1

MacromoleculeName: Gic1 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FMY1027 / synonym: Yeast
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: GTPase-interacting component 1

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Details: 100 mM NaCl, 20 mM mM Tris-HCl, 1 mM DTT
GridDetails: 400 Mesh 2/1 C-flat holey carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeOTHER
Specialist opticsEnergy filter - Name: in-column Omega filte / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
DateOct 28, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 63 / Average electron dose: 65 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 85470 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: -62 ° / Tilt series - Axis1 - Max angle: 62 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

DetailsStandard eTOMO procedures for single axis tilt tomograms
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 60.0 Å / Resolution method: OTHER / Software - Name: Imod / Number images used: 63

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