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- EMDB-19733: Cryo-EM structure of Arf1-decorated membrane tubules -

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Basic information

Entry
Database: EMDB / ID: EMD-19733
TitleCryo-EM structure of Arf1-decorated membrane tubules
Map data
Sample
  • Complex: Heptameric complex of Arf1 with GSP and Mg
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: water
KeywordsMembrane tubules / Arf1 / COPI / PROTEIN TRANSPORT / TRANSPORT PROTEIN
Function / homology
Function and homology information


Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / protein localization to Golgi membrane / regulation of Golgi organization / trans-Golgi Network Vesicle Budding / organelle membrane contact site / Intra-Golgi traffic / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / protein localization to Golgi membrane / regulation of Golgi organization / trans-Golgi Network Vesicle Budding / organelle membrane contact site / Intra-Golgi traffic / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / positive regulation of mitochondrial fusion / regulation of fatty acid metabolic process / Golgi to plasma membrane transport / positive regulation of mitochondrial fission / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / small monomeric GTPase / macroautophagy / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP-ribosylation factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHaupt C / Semchonok DA / Stubbs MT / Bacia K / Desfosses A / Kastritis PL / Hamdi F
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
CitationJournal: Cell Structure / Year: 2024
Title: Cryo-EM structure of Arf1-decorated membrane tubules
Authors: Haupt C / Semchonok DA / Stubbs MT / Bacia K / Desfosses A
History
DepositionFeb 23, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19733.png

Downloads & links

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Map

FileDownload / File: emd_19733.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.53 Å/pix.
x 384 pix.
= 587.677 Å		1.53 Å/pix.
x 384 pix.
= 587.677 Å		1.53 Å/pix.
x 384 pix.
= 587.677 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.53041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.0
Minimum - Maximum-279.330660000000023 - 554.632449999999949
Average (Standard dev.)-0.30801257 (±5.8531713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 587.6775 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19733_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_19733_additional_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_19733_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19733_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric complex of Arf1 with GSP and Mg

EntireName: Heptameric complex of Arf1 with GSP and Mg
Components
  • Complex: Heptameric complex of Arf1 with GSP and Mg
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: water

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Supramolecule #1: Heptameric complex of Arf1 with GSP and Mg

SupramoleculeName: Heptameric complex of Arf1 with GSP and Mg / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 1
Details: A myristoyl group (derived from myristic acid) is covalently attached to the N-terminus via an amide bond.
Number of copies: 7 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.552438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGLFASKLFS NLFGNKEMRI LMVGLDGAGK TTVLYKLKLG EVITTIPTIG FNVETVQYKN ISFTVWDVGG QDRIRSLWRH YYRNTEGVI FVVDSNDRSR IGEAREVMQR MLNEDELRNA AWLVFANKQD LPEAMSAAEI TEKLGLHSIR NRPWFIQATC A TSGEGLYE GLEWLSNSLK NST

UniProtKB: ADP-ribosylation factor 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

MacromoleculeName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: GSP
Molecular weightTheoretical: 539.246 Da
Chemical component information

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationName
20.0 mMHEPES
50.0 mMKOAc
1.2 mMMgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 77.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 12483 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1489051
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1) / Number images used: 485140
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 125000 / Software - Name: cryoSPARC (ver. v4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2ksq


Chain - Chain ID: A / Chain - Residue range: 16-178 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 94.1
Output model

PDB-8s5e:
Cryo-EM structure of Arf1-decorated membrane tubules

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