|Entry||Database: EMDB / ID: 7077|
|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||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:|
Cytohesin-3,ADP-ribosylation factor 6 / (ligand) x 3
|Function / homology||Sec7, C-terminal domain superfamily / Small GTPase superfamily, ARF/SAR type / PH-like domain superfamily / Small GTP-binding protein domain / Small GTPase superfamily, ARF type / P-loop containing nucleoside triphosphate hydrolase / Sec7 domain superfamily / ADP-ribosylation factor family / Pleckstrin homology domain / PH domain ...Sec7, C-terminal domain superfamily / Small GTPase superfamily, ARF/SAR type / PH-like domain superfamily / Small GTP-binding protein domain / Small GTPase superfamily, ARF type / P-loop containing nucleoside triphosphate hydrolase / Sec7 domain superfamily / ADP-ribosylation factor family / Pleckstrin homology domain / PH domain / Sec7 domain / PH domain profile. / SEC7 domain profile. / small GTPase Arf family profile. / TBC/RABGAPs / Clathrin-mediated endocytosis / Sec7 domain / MET receptor recycling / Intra-Golgi traffic / myeloid cell apoptotic process / protein localization to endosome / regulation of dendritic spine development / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / endocytic recycling / negative regulation of protein localization to cell surface / negative regulation of dendrite development / ARF guanyl-nucleotide exchange factor activity / regulation of filopodium assembly / Flemming body / protein localization to cell surface / thioesterase binding / filopodium membrane / cortical actin cytoskeleton organization / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / hepatocyte apoptotic process / positive regulation of cell adhesion / positive regulation of actin filament polymerization / adherens junction / guanyl-nucleotide exchange factor activity / bicellular tight junction / vesicle-mediated transport / endocytic vesicle / ruffle / liver development / positive regulation of protein localization to plasma membrane / recycling endosome membrane / cell cortex / protein transport / extrinsic component of cytoplasmic side of plasma membrane / protein N-terminus binding / early endosome / endosome / GTPase activity / cell cycle / cell division / cell adhesion / myelin sheath / GTP binding / focal adhesion / Golgi apparatus / membrane / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm / Cytohesin-3 / ADP-ribosylation factor 6|
Function and homology information
|Source||Mus musculus (house mouse)|
|Method||single particle reconstruction / negative staining / 35 Å resolution|
|Authors||Das S / Malaby AW|
|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.
|Validation Report||PDB-ID: 6bbp|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 19, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7077.map.gz (map file in CCP4 format, 2049 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.5 Å|
CCP4 map header:
+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|
Number of components: 5
+Component #1: protein, Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-39...
|Protein||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|
Recombinant expression: No
|Source||Species: Mus musculus (house mouse)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
+Component #2: protein, Cytohesin-3,ADP-ribosylation factor 6
|Protein||Name: Cytohesin-3,ADP-ribosylation factor 6 / Recombinant expression: No|
|Mass||Theoretical: 60.292777 kDa|
|Source (engineered)||Expression System: Homo sapiens (human)|
+Component #3: ligand, GUANOSINE-5'-TRIPHOSPHATE
|Ligand||Name: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 0.52318 kDa|
+Component #4: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
+Component #5: ligand, INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
|Ligand||Name: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 0.500075 kDa|
|Specimen||Specimen state: particle / Method: negative staining|
|Sample solution||Buffer solution: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4|
|Staining||Stained with 0.75% (w/v) uranyl formate|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 12|
Details: Gatan Erlang Shen 785 camera used for collecting images
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3200 nm|
|Specimen Holder||Model: OTHER|
|Image acquisition||Number of digital images: 369|
Details: Gatan Erlang Shen 785 camera used for collecting images
|Processing||Method: single particle reconstruction / Number of projections: 6504 / Details: The images were X-ray corrected|
|3D reconstruction||Software: EMAN / Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF|
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