8S5D

Cryo-EM structure of Arf1-decorated membrane tubules

• PDB DOI: https://doi.org/10.2210/pdb8S5D/pdb
• EM Map EMD-19732: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-23 Released: 2025-01-22 
• Deposition Author(s): Haupt, C., Semchonok, D.A., Stubbs, M.T., Bacia, K., Desfosses, A., Kastritis, P.L., Hamdi, F.
• Funding Organization(s): German Federal Ministry for Education and Research

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.79 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Cryo-EM structure of Arf1-decorated membrane tubules

Haupt, C., Semchonok, D.A., Stubbs, M.T., Bacia, K., Desfosses, A.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 241-mer - A241 

Biological assembly 1 assigned by authors and generated by UCSF CHIMERA 1.17.3_b42480. (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 21.12 kDa 
• Atom Count: 1,339 
• Modelled Residue Count: 163 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	A	181	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ARF1, YDL192W, D1244 EC: 3.6.5.2
UniProt
Find proteins for P11076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11076  Go to UniProtKB:  P11076

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP (Subject of Investigation/LOI)	C [auth A]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.79 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21-5187
MODEL REFINEMENT	Coot	0.9.7 EL
RECONSTRUCTION	cryoSPARC	v4.3.1, v4.4.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Haupt, C., Semchonok, D.A., Stubbs, M.T., Bacia, K., Desfosses, A., Kastritis, P.L., Hamdi, F.

---

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	03Z22HN23
German Federal Ministry for Education and Research	Germany	03Z22HI2

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release