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- EMDB-7078: Model for extended volume of truncated monomeric Cytohesin-3 (Grp... -

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Entry
Database: EMDB / ID: EMD-7078
TitleModel for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein
Map dataExtended volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein,
Sample
  • Complex: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
    • Protein or peptide: Cytohesin-3,ADP-ribosylation factor 6
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
KeywordsGuanine nucleotide exchange factor / Arf GTPase / Fusion protein / Inositol 1 / 3 / 4 / 5-tetrakisphosphate / LIPID BINDING PROTEIN
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / Intra-Golgi traffic / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / Intra-Golgi traffic / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / MET receptor recycling / endocytic recycling / thioesterase binding / Flemming body / filopodium membrane / TBC/RABGAPs / protein localization to cell surface / cortical actin cytoskeleton organization / hepatocyte apoptotic process / positive regulation of actin filament polymerization / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / endocytic vesicle / synaptic vesicle endocytosis / bicellular tight junction / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / small monomeric GTPase / positive regulation of protein secretion / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / recycling endosome membrane / GDP binding / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / early endosome membrane / cell cortex / cell differentiation / postsynapse / cell adhesion / endosome / cell division / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 6 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases ...ADP-ribosylation factor 6 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cytohesin-3 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 35.0 Å
AuthorsDas S / Malaby AW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 056324 United States
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.
History
DepositionOct 19, 2017-
Header (metadata) releaseJan 10, 2018-
Map releaseJan 10, 2018-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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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
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  • Surface view with fitted model
  • Atomic models: PDB-6bbq
  • Surface level: 0.0639
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7078.png

Downloads & links

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Map

FileDownload / File: emd_7078.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExtended volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein,
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0639 / Movie #1: 0.0639
Minimum - Maximum-0.81098795 - 2.976905
Average (Standard dev.)-0.0019418432 (±0.15161914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.8112.977-0.002

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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
Components
  • Complex: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
    • Protein or peptide: Cytohesin-3,ADP-ribosylation factor 6
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

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Supramolecule #1: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A ...

SupramoleculeName: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Cytohesin-3,ADP-ribosylation factor 6

MacromoleculeName: Cytohesin-3,ADP-ribosylation factor 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.307855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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 LTSNYK

UniProtKB: Cytohesin-3, ADP-ribosylation factor 6

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Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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

MacromoleculeName: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: 4IP
Molecular weightTheoretical: 500.075 Da
Chemical component information

ChemComp-4IP:
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Details: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
StainingType: NEGATIVE / Material: Uranyl Formate / Details: Stained with 0.75% (w/v) uranyl formate
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeFEI TECNAI 12
DetailsGatan Erlang Shen 785 camera used for collecting images
Image recordingFilm 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
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 60000

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Image processing

DetailsThe images were X-ray corrected
Particle selectionNumber selected: 10000 / Details: EMAN2 based manual particle picking
Startup modelType of model: NONE
Final reconstructionNumber classes used: 71 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 2) / Number images used: 6504
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 80 / Avg.num./class: 91 / Software - Name: EMAN (ver. 2)

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