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Yorodumi- EMDB-2504: Septin-Gic1-Cdc42-GppNHp complex in a single-tilt-axis subtomogram -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2504 | |||||||||
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Title | Septin-Gic1-Cdc42-GppNHp complex in a single-tilt-axis subtomogram | |||||||||
Map data | Cryo-Tomogram of Septin/Gic1/Cdc42-GppNHp Complex. | |||||||||
Sample |
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Keywords | cell 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 / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...septin ring organization / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / incipient cellular bud site / apolipoprotein A-I receptor binding / neuron fate determination / cellular bud tip / modulation by host of viral process / GTP-dependent protein binding / 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 / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / positive regulation of intracellular protein transport / cellular bud neck / cell junction assembly / mating projection tip / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / nuclear migration / regulation of lamellipodium assembly / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / establishment of cell polarity / phagocytosis, engulfment / heart contraction / positive regulation of DNA replication / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / 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 / EGFR downregulation / small monomeric GTPase / G protein activity / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCGR3A-mediated phagocytosis / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / G beta:gamma signalling through CDC42 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM / Resolution: 60.0 Å | |||||||||
Authors | Sadian Y / Gatsogiannis C / Patasi C / Hofnagel O / Goody RS / Farkasovsky M / Raunser S | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2504.map.gz | 11.1 MB | EMDB map data format | |
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Header (meta data) | emd-2504-v30.xml emd-2504.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_2504.jpg | 1.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2504 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2504 | HTTPS FTP |
-Validation report
Summary document | emd_2504_validation.pdf.gz | 172.6 KB | Display | EMDB validaton report |
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Full document | emd_2504_full_validation.pdf.gz | 171.7 KB | Display | |
Data in XML | emd_2504_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2504 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2504 | HTTPS FTP |
-Related structure data
Related structure data | 2505C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2504.map.gz / Format: CCP4 / Size: 13.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-Tomogram of Septin/Gic1/Cdc42-GppNHp Complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Septin-Gic1-Cdc42-GppNHp complex
Entire | Name: Septin-Gic1-Cdc42-GppNHp complex |
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Components |
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-Supramolecule #1000: Septin-Gic1-Cdc42-GppNHp complex
Supramolecule | Name: Septin-Gic1-Cdc42-GppNHp complex / type: sample / ID: 1000 / Number unique components: 3 |
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-Macromolecule #1: Septin
Macromolecule | Name: Septin / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FMY1027 / synonym: Yeast |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | InterPro: Septin |
-Macromolecule #2: Cell division control protein 42 homolog
Macromolecule | Name: Cell division control protein 42 homolog / type: protein_or_peptide / ID: 2 / Name.synonym: Cdc42 / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Sequence | UniProtKB: Cell division control protein 42 homolog |
-Macromolecule #3: Gic1
Macromolecule | Name: Gic1 / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FMY1027 / synonym: Yeast |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: GTPase-interacting component 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 / Details: 100 mM NaCl, 20 mM mM Tris-HCl, 1 mM DTT |
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Grid | Details: 400 Mesh 2/1 C-flat holey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Specialist optics | Energy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV |
Date | Jul 8, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 61 / Average electron dose: 65 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 85470 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 2 ° |
-Image processing
Details | Standard eTOMO procedures for single axis tilt tomograms |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 60.0 Å / Resolution method: OTHER / Software - Name: Imod / Number images used: 61 |