8S5E | pdb_00008s5e

Cryo-EM structure of Arf1-decorated membrane tubules

PDB DOI: https://doi.org/10.2210/pdb8S5E/pdb
EM Map EMD-19733: 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: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8S5E

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of Arf1-driven membrane tubulation

Haupt, C., Semchonok, D.A., Desfosses, A., Daum, S., Neudorf, S.S., Hamdi, F., Kastritis, P.L., Stubbs, M.T., Bacia, K.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.01.22.700998

Macromolecule Content

Total Structure Weight: 147.81 kDa
Atom Count: 9,373
Modeled Residue Count: 1,141
Deposited Residue Count: 1,267
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	A, B, C, D, E A, B, C, D, E, F, G	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11076
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSP (Subject of Investigation/LOI) Query on GSP Download:Ideal Coordinates CCD File SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ S XOFLBQFBSOEHOG-UUOKFMHZSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth G] SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth G] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth G] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F], T [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain T [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.3.1
MODEL REFINEMENT	PHENIX	1.21_5187

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Semchonok, D.A.

Kastritis, P.L.

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 (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release
Version 1.1: 2026-02-04
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.