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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 6
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
Keywordssmall GTPase / helical polymer / membrane tubulation / LIPID BINDING PROTEIN
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / 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 ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / 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 / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / MET receptor recycling / thioesterase binding / Flemming body / filopodium membrane / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / synaptic vesicle endocytosis / endocytic vesicle / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / liver development / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / cellular response to nerve growth factor stimulus / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / cell cortex / early endosome membrane / cell differentiation / postsynapse / endosome / cell adhesion / cell division / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADP-ribosylation factor 6 / 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 / 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: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission.
Authors: Xiaoyun Pang / Yan Zhang / Kunyou Park / Zhenyu Liao / Jian Li / Jiashu Xu / Minh-Triet Hong / Guoliang Yin / Tongming Zhang / Yaoyu Wang / Edward H Egelman / Jun Fan / Victor W Hsu / Seung- ...Authors: Xiaoyun Pang / Yan Zhang / Kunyou Park / Zhenyu Liao / Jian Li / Jiashu Xu / Minh-Triet Hong / Guoliang Yin / Tongming Zhang / Yaoyu Wang / Edward H Egelman / Jun Fan / Victor W Hsu / Seung-Yeol Park / Fei Sun /
Abstract: ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. We have pursued cryoelectron microscopy (EM) to reveal at 3.9 Å ...ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. We have pursued cryoelectron microscopy (EM) to reveal at 3.9 Å resolution how ARF6 assembles into a protein lattice on tubulated membrane. Molecular dynamics simulation studies confirm and extend the cryo-EM findings. The ARF6 lattice exhibits features that are distinct from those formed by other membrane-bending proteins. We identify protein contacts critical for lattice assembly and how membrane insertion results in constricted tubules. The lattice structure also enables docking by GTPase-activating proteins (GAP) to achieve vesiculation. We have also modeled ARF1 onto the ARF6 lattice, and then pursued vesicle reconstitution by the Coat Protein I (COPI) complex to further confirm that the ARF lattice acts in vesicle fission. By elucidating how an ARF protein tubulates membrane at the structural level, we have advanced the molecular understanding of how this class of transport factors promote the fission stage of vesicle formation.
History
DepositionMay 10, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
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 6
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-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

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

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Image processing

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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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