8SDW: Non-myristoylated mutant [L8K]Arf1

Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue. Determined by X-ray diffraction at 1.75 Å resolution. Released 28 Jun 2023.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,651
Mol. weight: 21.29 kDa
Ligands: G3D, MG
Released: 28 Jun 2023

Explore 8SDW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SDW contains 9 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-24	7	1
α-helix	30-37	8
α-helix	41-42	2
β-strand	43-48	6	1
β-strand	51-58	8	1
β-strand	61-67	7	1
α-helix	76-83	8
β-strand	87-93	7	1
α-helix	97-99	3
α-helix	100-111	12
α-helix	114-116	3
β-strand	120-126	7	1
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	1
β-strand	159	1	2
β-strand	164	1	2
α-helix	166-178	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 1	A	protein	181	Homo sapiens	P84077 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SDW_1 ADP-ribosylation factor 1 (chains A)
MGNIFANKFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN
ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAV
LLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ
K

Ligands and cofactors

ID	Name	Formula	Copies
G3D	Guanosine-3'-monophosphate-5'-diphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity. Rosenberg Jr., E.M., Jian, X., Soubias, O. et al. PLoS One (2024) 19:e0295103-e0295103. DOI 10.1371/journal.pone.0295103 · PubMed

Other PDB entries of the same protein (UniProt P84077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HUR 2.0 Å, Human ADP-ribosylation factor 1 complexed with GDP, full length non-myristoylated
7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
6FAE 2.35 Å, The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1
1RE0 2.4 Å, Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
7DN8 2.61 Å, Crystal structure of Salmonella effector SopF in complex with ARF1
9QLP 2.75 Å, NMT1-NAC bound human RNC with full length ARF1 - State 2
3O47 2.8 Å, Crystal structure of ARFGAP1-ARF1 fusion protein
7DN9 3.29 Å, Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1
6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
6DFF 3.9 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer

Browse structure collections

About this viewer

MolViewer shows 8SDW directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.