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- EMDB-7077: Model for compact volume of truncated monomeric Cytohesin-3 (Grp1... -

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Basic information

Entry
Database: EMDB / ID: 7077
TitleModel for compact volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
Map dataCompact volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
SampleTruncated 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 / homologySec7, 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
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / 35 Å resolution
AuthorsDas S / Malaby AW
CitationJournal: 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 ReportPDB-ID: 6bbp

SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0639
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0639
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bbp
  • Surface level: 0.0639
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7077.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density
Contour Level:0.0639 (by author), 0.0639 (movie #1):
Minimum - Maximum-0.87329674 - 3.578216
Average (Standard dev.)-0.0013035872 (0.1634007)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 280 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.8733.578-0.001

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Supplemental data

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Sample components

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Entire Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A ...

EntireName: 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

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Component #1: protein, Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-39...

ProteinName: 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
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Cytohesin-3,ADP-ribosylation factor 6

ProteinName: Cytohesin-3,ADP-ribosylation factor 6 / Recombinant expression: No
MassTheoretical: 60.292777 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #5: ligand, INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

LigandName: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.500075 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
pH: 8
StainingStained with 0.75% (w/v) uranyl formate
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Details: Gatan Erlang Shen 785 camera used for collecting images
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3200 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 369
Details: Gatan Erlang Shen 785 camera used for collecting images

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6504 / Details: The images were X-ray corrected
3D reconstructionSoftware: EMAN / Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Output model

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