+Open data
-Basic information
Entry | Database: PDB / ID: 7rx9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of autoinhibited P-Rex1 | |||||||||
Components | Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein, Endolysin chimera | |||||||||
Keywords | SIGNALING PROTEIN / P-Rex1 / P-Rex2 / GEF / cell growth / Rac1 / Cdc42 | |||||||||
Function / homology | Function and homology information regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle ...regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / viral release from host cell by cytolysis / RAC1 GTPase cycle / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / peptidoglycan catabolic process / neutrophil chemotaxis / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / growth cone / host cell cytoplasm / intracellular signal transduction / positive regulation of cell migration / defense response to bacterium / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | |||||||||
Authors | Ellisdon, A.M. / Chang, Y. | |||||||||
Funding support | Australia, 2items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism. Authors: Yong-Gang Chang / Christopher J Lupton / Charles Bayly-Jones / Alastair C Keen / Laura D'Andrea / Christina M Lucato / Joel R Steele / Hari Venugopal / Ralf B Schittenhelm / James C ...Authors: Yong-Gang Chang / Christopher J Lupton / Charles Bayly-Jones / Alastair C Keen / Laura D'Andrea / Christina M Lucato / Joel R Steele / Hari Venugopal / Ralf B Schittenhelm / James C Whisstock / Michelle L Halls / Andrew M Ellisdon / Abstract: P-Rex (PI(3,4,5)P-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by ...P-Rex (PI(3,4,5)P-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gβγ and PI(3,4,5)P binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126° opening of the DH domain hinge helix. The off-axis position of Gβγ and PI(3,4,5)P binding sites further suggests a counter-rotation of the P-Rex1 halves by 90° facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rx9.cif.gz | 221.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rx9.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/7rx9 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/7rx9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7syfC 4yonS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 70026.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: PREX1, KIAA1415 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TCU6, UniProt: P00720, lysozyme | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / Has ligand of interest | N | Sequence details | T4-Lysozyme is spliced/inserted into the P-Rex1 structure in a loop region to enable ...T4-Lysozyme is spliced/inserted into the P-Rex1 structure in a loop region to enable crystallisation. However, the T4L could not be built into the PDB model as it was too flexible. Density was present but too poor to build/model the T4L. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M (NH4)2SO4, 0.05 MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→47.83 Å / Num. obs: 18039 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 119.41 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.22→3.48 Å / Num. unique obs: 3597 / CC1/2: 0.358 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YON Resolution: 3.22→47.83 Å / SU ML: 0.4288 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4388 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 127.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.22→47.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|