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

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Basic information

Entry
Database: PDB / ID: 8s5e
TitleCryo-EM structure of Arf1-decorated membrane tubules
ComponentsADP-ribosylation factor 1
KeywordsTRANSPORT PROTEIN / Membrane tubules / Arf1 / COPI / PROTEIN TRANSPORT
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 / intracellular protein transport / macroautophagy / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHaupt, C. / Semchonok, D.A. / Stubbs, M.T. / Bacia, K. / Desfosses, A. / Kastritis, P.L. / Hamdi, F.
Funding support Germany, 2items
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, D.A. / Stubbs, M.T. / Bacia, K. / Desfosses, A.
History
DepositionFeb 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
B: ADP-ribosylation factor 1
C: ADP-ribosylation factor 1
D: ADP-ribosylation factor 1
E: ADP-ribosylation factor 1
F: ADP-ribosylation factor 1
G: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,81221
Polymers143,8677
Non-polymers3,94514
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ADP-ribosylation factor 1


Mass: 20552.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: A myristoyl group (derived from myristic acid) is covalently attached to the N-terminus via an amide bond.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARF1, YDL192W, D1244 / Production host: Escherichia coli (E. coli) / References: UniProt: P11076, small monomeric GTPase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heptameric complex of Arf1 with GSP and Mg / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.8
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
250 mMKOAc1
31.2 mMMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (min): 77 K
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12483
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
2EPU2.2.0.65RELimage acquisition
4cryoSPARCv4.3.1CTF correction
7PHENIX1.21_5187model fitting
8Coot0.9model fitting
9ISOLDE1.6model fitting
11cryoSPARCv4.3.1initial Euler assignment
12cryoSPARCv4.3.1final Euler assignment
13cryoSPARCv4.3.1classification
14cryoSPARCv4.3.13D reconstruction
15PHENIX1.21_5187model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1489051
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 485140 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 94.1 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 2ksq

2ksq


Pdb chain-ID: A / Accession code: 2ksq / Chain residue range: 16-178 / Pdb chain residue range: 16-178 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.019541
ELECTRON MICROSCOPYf_angle_d0.67112957
ELECTRON MICROSCOPYf_dihedral_angle_d20.6033087
ELECTRON MICROSCOPYf_chiral_restr0.0511428
ELECTRON MICROSCOPYf_plane_restr0.0051610

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