7XRD: Arf6 helical polymer assembled on lipid membrane

Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane. Determined by electron microscopy at 3.9 Å resolution. Released 15 Nov 2023.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,460
Mol. weight: 86.39 kDa
Ligands: GTP, MG
Released: 15 Nov 2023

Explore 7XRD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XRD contains 36 α-helices and 37 β-strands across 4 chains. 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	1
α-helix	26-35	10
β-strand	38-39	2	2
β-strand	46	1	3
β-strand	47-53	7	1
β-strand	57-64	8	1
α-helix	68-77	10
β-strand	83-89	7	1
α-helix	93-95	3
α-helix	96-107	12
α-helix	111-114	4
β-strand	116-122	7	1
α-helix	129-131	3
α-helix	132-139	8
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	155	1	4
β-strand	160	1	4
α-helix	162-171	10

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	3
α-helix	26-34	9
β-strand	39	1	5
β-strand	47-53	7	3
β-strand	57-64	8	3
α-helix	68-77	10
β-strand	83-89	7	3
α-helix	93-95	3
α-helix	96-107	12
α-helix	111-114	4
β-strand	116-122	7	3
α-helix	129-131	3
α-helix	132-139	8
α-helix	141-143	3
β-strand	149-153	5	3
β-strand	155	1	6
β-strand	160	1	6
α-helix	162-171	10

Chain C: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	7
α-helix	26-34	9
β-strand	39-40	2	2
β-strand	47-53	7	7
β-strand	57-64	8	7
α-helix	68-77	10
β-strand	83-89	7	7
α-helix	93-95	3
α-helix	96-107	12
α-helix	111-114	4
β-strand	116-122	7	7
α-helix	129-131	3
α-helix	132-138	7
α-helix	141-143	3
β-strand	149-153	5	7
β-strand	155	1	8
β-strand	160	1	8
α-helix	162-171	10

Chain D: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	9
α-helix	26-35	10
β-strand	39	1	5
β-strand	47-53	7	9
β-strand	57-64	8	9
α-helix	68-77	10
β-strand	83-89	7	9
α-helix	96-107	12
α-helix	111-114	4
α-helix	115	1
β-strand	116-122	7	9
α-helix	129-131	3
α-helix	132-139	8
α-helix	141-143	3
β-strand	149-153	5	9
β-strand	155	1	10
β-strand	160	1	10
α-helix	162-171	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 6	A, B, C, D	protein	182	Homo sapiens	P62330 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7XRD_1 ADP-ribosylation factor 6 (chains A, B, C, D)
GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNV
WDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFA
NKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKSLEHHHH
HH

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4
MG	Magnesium ion	Mg	4

Primary citation

Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission. Pang, X., Zhang, Y., Park, K. et al. Proc Natl Acad Sci U S A (2025) 122:e2417820122-e2417820122. DOI 10.1073/pnas.2417820122 · PubMed

Other PDB entries of the same protein (UniProt P62330 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A5D 1.8 Å, Structural basis for the activation of cholera toxin by human ARF6-GTP
3N5C 1.82 Å, Crystal Structure of Arf6DELTA13 complexed with GDP
4KAX 1.85 Å, Crystal structure of the Grp1 PH domain in complex with Arf6-GTP
2W83 1.93 Å, Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4
6PAU 1.93 Å, Structure of Human NMT2 with myristoyl-lysine peptide and CoA products
2A5F 2.02 Å, Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator,…
7RK3 2.05 Å, Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to…
1E0S 2.28 Å, small G protein Arf6-GDP
3PCR 2.5 Å, Structure of EspG-Arf6 complex
6PAV 2.52 Å, Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated…
2A5G 2.66 Å, Cholera toxin A1 subunit bound to ARF6(Q67L)
2J5X 2.8 Å, Structure of the small G protein ARF6 in complex with gtpgammas

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