7YIS: N-terminal PH domain of ARAP3 protein

Crystal structure of N-terminal PH domain of ARAP3 protein in complex with inositol 1,3,4,5-tetrakisphosphate. Determined by X-ray diffraction at 3.3 Å resolution. Released 3 May 2023.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 838
Mol. weight: 13.77 kDa
Ligands: 4PT
Released: 3 May 2023

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

Secondary structure: helices and β-sheets

7YIS contains 2 α-helices and 7 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	290-297	8	1
α-helix	298	1
β-strand	305-312	8	1
β-strand	316-320	5	1
β-strand	330-333	4	1
β-strand	337-342	6	1
β-strand	347-352	6	1
β-strand	356-360	5	1
α-helix	364-381	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3	A	protein	111	Homo sapiens	Q8WWN8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YIS_1 Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 (chains A)
MDRLTPLLSGWLDKLSPQGNYVFQRRFVQFNGRSLMYFGSDKDPFPKGVIPLTAIEMTRS
SKDNKFQVITGQRVFVFRTESEAQRDMWCSTLQSCLKEQRLLGLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
4PT	(2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]o…	C17 H36 O22 P4	1

Primary citation

Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3. Zhang, Y., Ge, L., Xu, L. et al. Int J Mol Sci (2023) 24. DOI 10.3390/ijms24021125 · PubMed

Other PDB entries of the same protein (UniProt Q8WWN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A9B 2.0 Å, Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide
7YIR 2.1 Å, Crystal structure of N-terminal PH domain of ARAP3 protein from human
5JCP 2.1 Å, RhoGAP domain of ARAP3 in complex with RhoA in the transition state
5JD0 2.3 Å, crystal structure of ARAP3 RhoGAP domain
2KG5 NMR Solution structure of ARAP3-SAM
2LNW Identification and structural basis for a novel interaction between Vav2 and Arap3

Browse structure collections

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