Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 607–706 | Fragment：UNP Residues 607-706 | UNX UNKNOWN LIGAND × 16 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate, pH 6.2, vapor diffusion, sitting drop, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1.2M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Soaked for 6 hours in 0.01 M potassium hexaiodoplatin-(IV)-ate and mother liquor, pH 5.6, vapor diffusion, sitting drop, temperature 293K | Resolution 2.29 Å R-free 0.269 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 3QIK | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4YON P-Rex1:Rac1 complex Deposited 2015-03-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–404（404 aa）
Fragment：UNP residues 1-404
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 sodium MES, pH 6.5, 0.2M sodium acetate, 15% (w/v) PEG 8000
|
Resolution 1.95 Å R-free 0.183 |
| 5D27 Crystal Structure of the P-Rex1 PH domain Deposited 2015-08-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
245–408（164 aa）
|
Not recorded | NI NICKEL (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Magnesium chloride, PEG 3350
|
Resolution 1.92 Å R-free 0.232 |
| 5D3V Crystal Structure of the P-Rex1 PH domain with Citrate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；Sodium citrate, PEG 8000
|
Resolution 1.85 Å R-free 0.215 |
| 5D3V Crystal Structure of the P-Rex1 PH domain with Citrate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；Sodium citrate, PEG 8000
|
Resolution 1.85 Å R-free 0.215 |
| 5D3W Crystal Structure of the P-Rex1 PH domain with Sulfate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Ammonium sulfate, PEG 3350
|
Resolution 1.85 Å R-free 0.215 |
| 5D3W Crystal Structure of the P-Rex1 PH domain with Sulfate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；294 K；Bis Tris, Ammonium sulfate, PEG 3350
|
Resolution 1.85 Å R-free 0.215 |
| 5D3X Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；HEPES, Jeffamine ED-2001 pH 7
|
Resolution 1.69 Å R-free 0.214 |
| 5D3X Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；HEPES, Jeffamine ED-2001 pH 7
|
Resolution 1.69 Å R-free 0.214 |
| 5D3Y Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；Bis Tris, polypropylene glycol P400
|
Resolution 1.95 Å R-free 0.258 |
| 5D3Y Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound Deposited 2015-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
245–408（164 aa）
Fragment：unp residues 245-408
|
Not recorded | 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；Bis Tris, polypropylene glycol P400
|
Resolution 1.95 Å R-free 0.258 |
| 5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
38–201（164 aa）
Chain A
202–408（207 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000
|
Resolution 3.28 Å R-free 0.235 |
| 5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
38–201（164 aa）
Chain C
202–408（207 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000
|
Resolution 3.28 Å R-free 0.235 |
| 5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
38–201（164 aa）
Chain E
202–408（207 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000
|
Resolution 3.28 Å R-free 0.235 |
| 5FI0 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 Deposited 2015-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
38–201（164 aa）
Chain G
202–408（207 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；Sodium dihydrogen phosphate, PEG 8000
|
Resolution 3.28 Å R-free 0.235 |
| 5FI1 Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 Deposited 2015-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
38–201（164 aa）
Chain A
202–408（207 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Ammonium citrate, PEG 3350
|
Resolution 3.20 Å R-free 0.198 |
| 6VSK Crystal structure of the P-Rex1 DEP1 domain Deposited 2020-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
409–499（91 aa）
Fragment：P-Rex1DEP1 domain (UNP residues 409-499)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M HEPES, pH 6.5, 45% w/v poly(acrylic acid sodium salt)2100
|
Resolution 3.12 Å R-free 0.233 |
| 7RX9 Structure of autoinhibited P-Rex1 Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–305（265 aa）
Chain A
323–502（180 aa）
|
Not recorded | SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M (NH4)2SO4, 0.05 MES pH 6.0
|
Resolution 3.22 Å R-free 0.262 |
| 7SYF Reconstruction of full-length Prex-1 (PtdIns(3,4,5)P3-dependent Rac Exchanger 1) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–305（265 aa）
Chain A
323–1117（795 aa）
Chain A
1212–1659（448 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8TUA Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4) Deposited 2023-08-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
35–1659（1625 aa）
|
Not recorded | 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
12 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PREX1_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–101； UniProt 607–706 |