6VSK: P-Rex1 DEP1 domain

Crystal structure of the P-Rex1 DEP1 domain. Determined by X-ray diffraction at 3.12 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 1
Atoms: 754
Mol. weight: 10.97 kDa
Released: 22 Jul 2020

Explore 6VSK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VSK contains 4 α-helices and 0 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	408-421	14
α-helix	436-438	3
α-helix	444-453	10
α-helix	460-472	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein	A	protein	94	Homo sapiens	Q8TCU6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VSK_1 Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein (chains A)
SNAIAEKGEKLYHMMMNKKVNLIKDRRRKLSTVPKCFLGNEFVAWLLEIGEISKTEEGVN
LGQALLENGIIHHVSDKHQFKNEQVMYRFRYDDG

Primary citation

The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding. Ravala, S.K., Hopkins, J.B., Plescia, C.B. et al. J Biol Chem (2020) 295:12635-12647. DOI 10.1074/jbc.RA120.014534 · PubMed

Other PDB entries of the same protein (UniProt Q8TCU6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D3X 1.69 Å, Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
5D3V 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Citrate Bound
5D3W 1.85 Å, Crystal Structure of the P-Rex1 PH domain with Sulfate Bound
5D27 1.92 Å, Crystal Structure of the P-Rex1 PH domain
4YON 1.95 Å, P-Rex1:Rac1 complex
5D3Y 1.95 Å, Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
3QIK 2.29 Å, Crystal structure of the first PDZ domain of PREX1
6PCV 3.2 Å, Single Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent…
5FI1 3.2 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42
7RX9 3.22 Å, Structure of autoinhibited P-Rex1
5FI0 3.28 Å, Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1
8TUA 4.1 Å, Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)

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