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- EMDB-19732: Cryo-EM structure of Arf1-decorated membrane tubules -

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Basic information

Entry
Database: EMDB / ID: EMD-19732
TitleCryo-EM structure of Arf1-decorated membrane tubules
Map datamap_sharp
Sample
  • Complex: Arf1 coated membrane tubules
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: water
KeywordsArf1 / protein-membrane interaction / membrane tubules / helical structure / 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 / Intra-Golgi traffic / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / regulation of Golgi organization / organelle membrane contact site / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport ...Synthesis of PIPs at the plasma membrane / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / regulation of Golgi organization / organelle membrane contact site / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi vesicle 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 / intracellular protein transport / macroautophagy / GTPase activity / GTP binding / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / 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 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.79 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: To Be Published
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_19732.png

Downloads & links

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Map

FileDownload / File: emd_19732.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap_sharp
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.53041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0
Minimum - Maximum-45.496229999999997 - 101.428479999999993
Average (Standard dev.)0.09014437 (±5.349479)
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_19732_msk_1.map
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Additional map: map sym

Fileemd_19732_additional_1.map
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Additional map: map sym sharp

Fileemd_19732_additional_2.map
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Additional map: map

Fileemd_19732_additional_3.map
Annotationmap
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Half map: B

Fileemd_19732_half_map_1.map
AnnotationB
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Half map: A

Fileemd_19732_half_map_2.map
AnnotationA
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Sample components

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Entire : Arf1 coated membrane tubules

EntireName: Arf1 coated membrane tubules
Components
  • Complex: Arf1 coated membrane tubules
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: water

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Supramolecule #1: Arf1 coated membrane tubules

SupramoleculeName: Arf1 coated membrane tubules / 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: 1 / 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: 1 / 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: 1 / 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: 2 / 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
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
50.0 mMKAcpotassium acetate
1.2 mMMgCl2magnesium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / 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
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: 21.0 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 5.821 Å
Applied symmetry - Helical parameters - Δ&Phi: 20.78 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1, v4.4.2) / Number images used: 27285
Segment selectionNumber selected: 1489051 / Software - Name: cryoSPARC (ver. v4.3.1, v4.4.2)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ksq

Final angle assignmentType: NOT APPLICABLE
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
Output model

PDB-8s5d:
Cryo-EM structure of Arf1-decorated membrane tubules

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