5FI0: P-Rex1 DH/PH tandem

Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1. Determined by X-ray diffraction at 3.28 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 3.28 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,731
Mol. weight: 259.89 kDa
Ligands: PO4
Released: 20 Apr 2016

Explore 5FI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FI0 contains 113 α-helices and 64 β-strands across 8 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: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	38-71	34
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-87	5
α-helix	93-100	8
α-helix	103-120	18
α-helix	132-138	7
α-helix	141-143	3
α-helix	144-162	19
α-helix	166-178	13
α-helix	188-211	24
α-helix	220-255	36
β-strand	257-258	2	1
α-helix	265-268	4
β-strand	272-281	10	1
β-strand	286-294	9	1
β-strand	297-303	7	1
β-strand	325-332	8	1
α-helix	333-335	3
β-strand	336-340	5	1
β-strand	345	1	2
β-strand	355	1	2
β-strand	358-363	6	1
α-helix	364-366	3
β-strand	368-373	6	1
α-helix	377-397	21

Chain B: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	3
α-helix	16-25	10
α-helix	33-34	2
β-strand	40-46	7	3
β-strand	49-57	9	3
α-helix	61-63	3
α-helix	68-71	4
β-strand	77-83	7	3
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	3
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	3
α-helix	165-177	13

Chain C: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	39-71	33
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-87	5
α-helix	93-100	8
α-helix	103-120	18
α-helix	132-138	7
α-helix	141-143	3
α-helix	144-162	19
α-helix	166-178	13
α-helix	188-199	12
α-helix	202-211	10
α-helix	220-255	36
β-strand	257-258	2	4
α-helix	265-268	4
β-strand	272-281	10	4
β-strand	286-294	9	4
β-strand	297-303	7	4
β-strand	325-332	8	4
α-helix	333-335	3
β-strand	336-340	5	4
β-strand	345	1	5
β-strand	355	1	5
β-strand	358-363	6	4
α-helix	364-366	3
β-strand	368-373	6	4
α-helix	377-398	22

Chain D: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
α-helix	16-24	9
α-helix	33-34	2
β-strand	40-46	7	6
β-strand	49-57	9	6
α-helix	68-71	4
β-strand	77-83	7	6
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	6
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	6
α-helix	165-177	13

Chain E: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	-1-71	36
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-89	7
α-helix	93-100	8
α-helix	103-120	18
α-helix	132-138	7
α-helix	141-143	3
α-helix	144-162	19
α-helix	166-178	13
α-helix	188-199	12
α-helix	202-211	10
α-helix	220-255	36
β-strand	257-258	2	7
α-helix	265-268	4
β-strand	272-281	10	7
β-strand	286-294	9	7
β-strand	297-303	7	7
β-strand	325-332	8	7
β-strand	336-340	5	7
β-strand	345	1	8
β-strand	355	1	8
β-strand	358-363	6	7
α-helix	364-366	3
β-strand	368-373	6	7
α-helix	377-396	20

Chain F: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-10	8	9
α-helix	16-25	10
α-helix	33-34	2
β-strand	40-46	7	9
β-strand	49-56	8	9
α-helix	61-63	3
α-helix	68-71	4
β-strand	77-83	7	9
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	9
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	9
α-helix	165-177	13

Chain G: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	0-71	35
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-89	7
α-helix	93-100	8
α-helix	103-120	18
α-helix	132-138	7
α-helix	141-143	3
α-helix	144-162	19
α-helix	166-178	13
α-helix	188-199	12
α-helix	202-211	10
α-helix	220-255	36
β-strand	257-258	2	10
α-helix	265-268	4
β-strand	272-281	10	10
β-strand	286-294	9	10
β-strand	297-303	7	10
β-strand	325-332	8	10
β-strand	336-340	5	10
β-strand	345	1	11
β-strand	355	1	11
β-strand	358-363	6	10
α-helix	364-366	3
β-strand	368-373	6	10
α-helix	377-396	20

Chain H: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	12
α-helix	16-24	9
α-helix	33-34	2
β-strand	40-46	7	12
β-strand	49-56	8	12
α-helix	61-63	3
α-helix	68-71	4
β-strand	77-83	7	12
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	12
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	153-156	4	12
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol…	A, C, E, G	protein	374	Homo sapiens	Q8TCU6 (AlphaFold model)
Ras-related C3 botulinum toxin substrate 1	B, D, F, H	protein	195	Homo sapiens	P63000 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5FI0_1 Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein (chains A, C, E, G)
GEFAAARESERQLRLRLCVLNEILGTERDYVGTLRFLQSAFLHRIRQNVADSVEKGLTEE
NVKVLFSNIEDILEVHKDFLAALEYCLHPEPQSQHELGNVFLKFKDKFCVYEEYCSNHEK
ALRLLVELNKIPTVRAFLLSCMLLGGRKTTDIPLEGYLLSPIQRICKYPLLLKELAKRTP
GKHPDHPAVQSALQAMKTVCSNINETKRQMEKLEALEQLQSHIEGWEGSNLTDICTQLLL
QGTLLKISAGNIQERAFFLFDNLLVYCKRKSRVTGSKKSTKRTKSINGSLYIFRGRINTE
VMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQR
ESLKLGMERDAYVM

Sequence of entity 2 (B, D, F, H), FASTA

>5FI0_2 Ras-related C3 botulinum toxin substrate 1 (chains B, D, F, H)
GEFMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWD
TAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKL
DLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
CPPPVKKRKRKCLLL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

Primary citation

Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3. Cash, J.N., Davis, E.M., Tesmer, J.J. Structure (2016) 24:730-740. DOI 10.1016/j.str.2016.02.022 · 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
6VSK 3.12 Å, Crystal structure of the P-Rex1 DEP1 domain
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
8TUA 4.1 Å, Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)

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