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- EMDB-33414: Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-33414
TitleCryo-EM structure of Arf6 helical polymer assembled on lipid membrane
Map data
Sample
  • Complex: Arf6 helical polymer assembled on lipid membrane
    • Protein or peptide: ADP-ribosylation factor 6ARF6
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
Keywordssmall GTPase / helical polymer / membrane tubulation / LIPID BINDING PROTEIN
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / negative regulation of receptor-mediated endocytosis / establishment of epithelial cell polarity / protein localization to endosome / ruffle assembly / negative regulation of dendrite development / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / negative regulation of receptor-mediated endocytosis / establishment of epithelial cell polarity / protein localization to endosome / ruffle assembly / negative regulation of dendrite development / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction / 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 / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / ruffle / 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 / 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 / membrane / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 6 / 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPang XY / Zhang Y / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane
Authors: Pang XY / Zhang Y / Sun F / Egelman E
History
DepositionMay 10, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33414.png

Downloads & links

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Map

FileDownload / File: emd_33414.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-10.259264 - 20.347511000000001
Average (Standard dev.)0.000000000003119 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Arf6 helical polymer assembled on lipid membrane

EntireName: Arf6 helical polymer assembled on lipid membrane
Components
  • Complex: Arf6 helical polymer assembled on lipid membrane
    • Protein or peptide: ADP-ribosylation factor 6ARF6
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

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Supramolecule #1: Arf6 helical polymer assembled on lipid membrane

SupramoleculeName: Arf6 helical polymer assembled on lipid membrane / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ADP-ribosylation factor 6

MacromoleculeName: ADP-ribosylation factor 6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.050121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKVLSKIFGN KEMRILMLGL DAAGKTTILY KLKLGQSVTT IPTVGFNVET VTYKNVKFNV WDVGGQDKIR PLWRHYYTGT QGLIFVVDC ADRDRIDEAR QELHRIINDR EMRDAIILIF ANKQDLPDAM KPHEIQEKLG LTRIRDRNWY VQPSCATSGD G LYEGLTWL TSNYKSLEHH HHHH

UniProtKB: ADP-ribosylation factor 6

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 28.01 Å
Applied symmetry - Helical parameters - Δ&Phi: 27.28 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20820
FSC plot (resolution estimation)

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