2W83: ARF6 GTPase

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4. Determined by X-ray diffraction at 1.93 Å resolution. Released 14 Jul 2009.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: HOMO SAPIENS
Chains: 5
Atoms: 5,359
Mol. weight: 76.99 kDa
Ligands: GTP, MG, DIO
Released: 14 Jul 2009

Explore 2W83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W83 contains 29 α-helices and 24 β-strands across 5 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	43-44	2
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	132-135	4
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	155	1	2
β-strand	160	1	2
α-helix	162-171	10

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	3
α-helix	26-35	10
α-helix	43-44	2
β-strand	47-53	7	3
β-strand	58-64	7	3
α-helix	68-77	10
β-strand	83-89	7	3
α-helix	93-95	3
α-helix	96-107	12
α-helix	110-112	3
β-strand	116-122	7	3
α-helix	132-138	7
β-strand	149-153	5	3
β-strand	155	1	4
β-strand	160	1	4
α-helix	162-171	10

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	389-451	63

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	392-451	60

Chain E: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	5
α-helix	26-35	10
β-strand	47-54	8	5
β-strand	57-64	8	5
α-helix	68-77	10
β-strand	83-89	7	5
α-helix	93-95	3
α-helix	96-107	12
α-helix	110-112	3
β-strand	116-122	7	5
α-helix	129-131	3
α-helix	132-138	7
α-helix	141-143	3
β-strand	149-153	5	5
β-strand	155	1	6
β-strand	160	1	6
α-helix	162-171	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 6	A, B, E	protein	165	HOMO SAPIENS	P62330 (AlphaFold model)
C-jun-amino-terminal kinase-interacting protein 4	C, D	protein	77	HOMO SAPIENS	O60271 (AlphaFold model)

Sequence of entity 1 (A, B, E), FASTA

>2W83_1 ADP-RIBOSYLATION FACTOR 6 (chains A, B, E)
AMEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKI
RPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAM
KPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

Sequence of entity 2 (C, D), FASTA

>2W83_2 C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4 (chains C, D)
AMDPEFMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAK
LKLEEKNRELEEELRKA

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	3
MG	Magnesium ion	Mg	3
DIO	1,4-diethylene dioxide	C4 H8 O2	6

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

Primary citation

The Structural Basis of Arf Effector Specificity: The Crystal Structure of Arf6 in a Complex with Jip4. Isabet, T., Montagnac, G., Regazzoni, K. et al. EMBO J (2009) 28:2835. DOI 10.1038/EMBOJ.2009.209 · 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
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

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