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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: EMD-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
Sample
  • Complex: 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
    • 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 / Intra-Golgi traffic / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / protein localization to endosome ...erythrocyte apoptotic process / Intra-Golgi traffic / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / protein localization to endosome / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / regulation of ARF protein signal transduction / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MET receptor recycling / endocytic recycling / thioesterase binding / Flemming body / TBC/RABGAPs / filopodium membrane / protein localization to cell surface / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / bicellular tight junction / signaling adaptor activity / vesicle-mediated transport / ruffle / positive regulation of cell adhesion / liver development / cellular response to nerve growth factor stimulus / small monomeric GTPase / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / adherens junction / intracellular protein transport / G protein activity / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Clathrin-mediated endocytosis / presynapse / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / cell differentiation / cell adhesion / endosome / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
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 family 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 family 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 6, 2024-
Current statusNov 6, 2024Processing 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-6bbp
  • Surface level: 0.0639
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7077.png

Downloads & links

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Map

FileDownload / File: emd_7077.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCompact 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-0.87329674 - 3.578216
Average (Standard dev.)-0.0013035872 (±0.1634007)
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-0.8733.578-0.001

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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
Components
  • Complex: 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
    • 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 complex with GTP, Mg and Inositol 1,3,4,5 tetrakisphosphate
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: 60.292777 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 LTSNYN

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 / 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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