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Yorodumi- EMDB-7077: Model for compact volume of truncated monomeric Cytohesin-3 (Grp1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7077 | |||||||||
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Title | Model for compact volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein | |||||||||
Map data | Compact volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein | |||||||||
Sample |
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Keywords | Guanine nucleotide exchange factor / Arf GTPase / Fusion protein / Inositol 1 / 3 / 4 / 5-tetrakisphosphate / LIPID BINDING PROTEIN | |||||||||
Function / homology | Function and homology information Intra-Golgi traffic / erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of ARF protein signal transduction / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development ...Intra-Golgi traffic / erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of ARF protein signal transduction / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / regulation of Rac protein signal transduction / negative regulation of protein localization to cell surface / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / thioesterase binding / MET receptor recycling / filopodium membrane / protein localization to cell surface / Flemming body / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / positive regulation of cell adhesion / bicellular tight junction / signaling adaptor activity / vesicle-mediated transport / ruffle / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / adherens junction / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / postsynapse / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 35.0 Å | |||||||||
Authors | Das S / Malaby AW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2018 Title: Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. Authors: Andrew W Malaby / Sanchaita Das / Srinivas Chakravarthy / Thomas C Irving / Osman Bilsel / David G Lambright / Abstract: Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and ...Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site. | |||||||||
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_7077.map.gz | 310.1 KB | EMDB map data format | |
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Header (meta data) | emd-7077-v30.xml emd-7077.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_7077.png | 20.7 KB | ||
Filedesc metadata | emd-7077.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7077 | HTTPS FTP |
-Related structure data
Related structure data | 6bbpMC 7078C 6bbqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7077.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Compact volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.5 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 : Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A ...
Entire | Name: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein complex with GTP, Mg and Inositol 1,3,4,5 tetrakisphosphate |
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Components |
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-Supramolecule #1: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A ...
Supramolecule | Name: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein complex with GTP, Mg and Inositol 1,3,4,5 tetrakisphosphate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Cytohesin-3,ADP-ribosylation factor 6
Macromolecule | Name: Cytohesin-3,ADP-ribosylation factor 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.292777 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHHHHHHGS TTQRNKQIAM GRKKFNMDPK KGIQFLIEND LLQSSPEDVA QFLYKGEGLN KTVIGDYLGE RDDFNIKVLQ AFVELHEFA DLNLVQALRQ FLWSFRLPGE AQKIDRMMEA FASRYCLCNP GVFQSTDTCY VLSFAIIMLN TSLHNHNVRD K PTAERFIT ...String: MGHHHHHHGS TTQRNKQIAM GRKKFNMDPK KGIQFLIEND LLQSSPEDVA QFLYKGEGLN KTVIGDYLGE RDDFNIKVLQ AFVELHEFA DLNLVQALRQ FLWSFRLPGE AQKIDRMMEA FASRYCLCNP GVFQSTDTCY VLSFAIIMLN TSLHNHNVRD K PTAERFIT MNRGINEGGD LPEELLRNLY ESIKNEPFKI PEDDGNDLTH TFFNPDREGW LLKLGGRVKT WKRRWFILTD NC LYYFEYT TDKEPRGIIP LENLSIREVE DPRKPNCFEL YNPSHKGQVI KACKTEADGR VVEGNHVVYR ISAPSPEEKE EWM KSIKAS ISRDPFYDML ATRKRRIANK KGKVLSKIFG NKEMRILMLG LDAAGKTTIL YKLKLGQSVT TIPTVGFNVE TVTY KNVKF NVWDVGGLDK IRPLWRHYYT GTQGLIFVVD CADRDRIDEA RQELHRIIND REMRDAIILI FANKQDLPDA MKPHE IQEK LGLTRIRDRN WYVQPSCATS GDGLYEGLTW LTSNYN UniProtKB: Cytohesin-3, ADP-ribosylation factor 6 |
-Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
Macromolecule | Name: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: 4IP |
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Molecular weight | Theoretical: 500.075 Da |
Chemical component information | ChemComp-4IP: |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: Stained with 0.75% (w/v) uranyl formate |
Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 60000 |
Details | Gatan Erlang Shen 785 camera used for collecting images |
Image recording | Film or detector model: OTHER / Number grids imaged: 1 / Number real images: 369 / Average electron dose: 20.0 e/Å2 Details: Gatan Erlang Shen 785 camera used for collecting images |
-Image processing
Particle selection | Number selected: 10000 / Details: EMAN2 based manual particle picking |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Number classes: 80 / Avg.num./class: 91 / Software - Name: EMAN (ver. 2) |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Number classes used: 71 / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 2) / Number images used: 6504 |
Details | The images were X-ray corrected |