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- EMDB-2504: Septin-Gic1-Cdc42-GppNHp complex in a single-tilt-axis subtomogram -

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Basic information

Entry
Database: EMDB / ID: EMD-2504
TitleSeptin-Gic1-Cdc42-GppNHp complex in a single-tilt-axis subtomogram
Map dataCryo-Tomogram of Septin/Gic1/Cdc42-GppNHp Complex.
Sample
  • Sample: Septin-Gic1-Cdc42-GppNHp complex
  • Protein or peptide: Septin
  • Protein or peptide: Cell division control protein 42 homolog
  • Protein or peptide: Gic1
Keywordscell division / bud neck filaments / cytokinesis / cytoskeleton / electron tomography / septin / gic / cdc42
Function / homology
Function and homology information


septin ring organization / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / dendritic cell migration ...septin ring organization / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / incipient cellular bud site / apolipoprotein A-I receptor binding / cellular bud tip / neuron fate determination / GTP-dependent protein binding / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / regulation of exit from mitosis / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of intracellular protein transport / neuropilin signaling pathway / cellular bud neck / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / mating projection tip / dendritic spine morphogenesis / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / thioesterase binding / embryonic heart tube development / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / sprouting angiogenesis / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / phagocytosis, engulfment / establishment of cell polarity / establishment or maintenance of cell polarity / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / secretory granule / positive regulation of DNA replication / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / G protein activity / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon
Similarity search - Function
Septin / Cdc42 / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Septin / Cdc42 / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTPase-interacting component 1 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human)
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: 126
  • 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_2504.jpg

Downloads & links

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Map

FileDownload / File: emd_2504.map.gz / Format: CCP4 / Size: 13.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-Tomogram of Septin/Gic1/Cdc42-GppNHp Complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 200 pix.
= 1440. Å		7.2 Å/pix.
x 120 pix.
= 864. Å		7.2 Å/pix.
x 148 pix.
= 1065.6 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 - Maximum90.753128050000001 - 154.714752199999992
Average (Standard dev.)117.257873540000006 (±4.64287663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-65654
Dimensions120148200
Spacing120148200
CellA: 1065.6 Å / B: 864.0 Å / C: 1440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z148120200
origin x/y/z0.0000.0000.000
length x/y/z1065.600864.0001440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-656-22454
NC/NR/NS148120200
D min/max/mean90.753154.715117.258

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Supplemental data

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Sample components

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Entire : Septin-Gic1-Cdc42-GppNHp complex

EntireName: Septin-Gic1-Cdc42-GppNHp complex
Components
  • Sample: Septin-Gic1-Cdc42-GppNHp complex
  • Protein or peptide: Septin
  • Protein or peptide: Cell division control protein 42 homolog
  • Protein or peptide: Gic1

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Supramolecule #1000: Septin-Gic1-Cdc42-GppNHp complex

SupramoleculeName: Septin-Gic1-Cdc42-GppNHp complex / type: sample / ID: 1000 / Number unique components: 3

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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: Cell division control protein 42 homolog

MacromoleculeName: Cell division control protein 42 homolog / type: protein_or_peptide / ID: 2 / Name.synonym: Cdc42 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human
SequenceUniProtKB: Cell division control protein 42 homolog

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Macromolecule #3: Gic1

MacromoleculeName: Gic1 / type: protein_or_peptide / ID: 3 / 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

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
DateJul 8, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 61 / 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: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / 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: 61

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