2A5D: ADP-ribosylation factor 6

Structural basis for the activation of cholera toxin by human ARF6-GTP. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Aug 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Vibrio cholerae
Chains: 2
Atoms: 3,102
Mol. weight: 42.48 kDa
Ligands: MG, GTP
Released: 16 Aug 2005

Explore 2A5D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2A5D contains 27 α-helices and 20 β-strands across 2 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	1
α-helix	26-35	10
α-helix	39-41	3
β-strand	47-54	8	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	110-112	3
β-strand	116-122	7	1
α-helix	129-131	3
α-helix	132-138	7
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	155	1	2
β-strand	160	1	2
α-helix	162-172	11

Chain B: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	3
α-helix	13-19	7
β-strand	21-22	2	4
α-helix	25-33	9
α-helix	35-37	3
β-strand	38	1	5
α-helix	41-46	6
β-strand	57	1	5
β-strand	59-63	5	3
α-helix	66-76	11
β-strand	82-89	8	3
β-strand	94-96	3	3
α-helix	97-101	5
α-helix	102-104	3
α-helix	108-110	3
β-strand	112-116	5	3
β-strand	119-120	2	4
α-helix	121-123	3
β-strand	124-131	8	3
β-strand	134	1	3
α-helix	138-139	2
β-strand	140-141	2	3
α-helix	147-150	4
α-helix	155-157	3
α-helix	158-161	4
α-helix	162-164	3
α-helix	172-175	4
α-helix	179-182	4
α-helix	183-184	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 6	A	protein	175	Homo sapiens	P62330 (AlphaFold model)
Cholera enterotoxin, A chain	B	protein	193	Vibrio cholerae	P01555 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2A5D_1 ADP-ribosylation factor 6 (chains A)
MGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFN
VWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIF
ANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

Sequence of entity 2 (B), FASTA

>2A5D_2 Cholera enterotoxin, A chain (chains B)
SNDDKLYRADSRPPDEIKQSGGLMPRGQSEYFDRGTQMNINLYDHARGTQTGFVRHDDGY
VSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDDQDVSALGGI
PYSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPW
IHHAPPGSGNAPR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Water and common crystallization additives (NA, GOL) are not listed.

Primary citation

Structural basis for the activation of cholera toxin by human ARF6-GTP. O'Neal, C.J., Jobling, M.G., Holmes, R.K. et al. Science (2005) 309:1093-1096. DOI 10.1126/science.1113398 · PubMed

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

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
3LVQ 3.38 Å, The crystal structure of ASAP3 in complex with Arf6 in transition state

Browse structure collections

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