4KAX: Grp1 PH domain

Crystal structure of the Grp1 PH domain in complex with Arf6-GTP. Determined by X-ray diffraction at 1.85 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,026
Mol. weight: 40.22 kDa
Ligands: GTP, MG, CIT, 4IP
Released: 14 Aug 2013

Explore 4KAX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KAX contains 12 α-helices and 19 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	1
α-helix	26-35	10
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
β-strand	149-153	5	1
β-strand	155	1	2
β-strand	160	1	2
α-helix	162-172	11

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	259-262	4
β-strand	267-274	8	3
β-strand	281-289	9	3
β-strand	292-296	5	3
β-strand	306-309	4	3
β-strand	311	1	4
β-strand	314-318	5	3
β-strand	326-330	5	3
α-helix	337-340	4
β-strand	342-344	3	3
β-strand	350-352	3	3
β-strand	358-361	4	3
α-helix	365-378	14
β-strand	380	1	4
α-helix	383-395	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 6	A	protein	169	Homo sapiens	P62330 (AlphaFold model)
Cytohesin-3	B	protein	161	Homo sapiens	O43739 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4KAX_1 ADP-ribosylation factor 6 (chains A)
HHHHHHGSMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVG
GLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQD
LPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYN

Sequence of entity 2 (B), FASTA

>4KAX_2 Cytohesin-3 (chains B)
HHHHHHGSPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEY
TTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVY
RISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIANKK

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
CIT	Citric acid	C6 H8 O7	1
4IP	Inositol-(1,3,4,5)-tetrakisphosphate	C6 H16 O18 P4	1

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

Primary citation

Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Malaby, A.W., van den Berg, B., Lambright, D.G. Proc Natl Acad Sci U S A (2013) 110:14213-14218. DOI 10.1073/pnas.1301883110 · 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
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

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