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Yorodumi- EMDB-25525: Localised reconstruction of the N-terminal half of P-Rex1 (PI(3,4... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25525 | |||||||||
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Title | Localised reconstruction of the N-terminal half of P-Rex1 (PI(3,4,5)P3-dependent Rac Exchanger 1) | |||||||||
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Sample |
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Keywords | guanine nucleotide exchange factor / metastasis / plasma membrane / Rho GTPase signalling / ONCOPROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Lupton CJ / Bayly-Jones C / Ellisdon AM | |||||||||
Funding support | Australia, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25525.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-25525-v30.xml emd-25525.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25525_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_25525.png | 39.4 KB | ||
Masks | emd_25525_msk_1.map | 14.5 MB | Mask map | |
Filedesc metadata | emd-25525.cif.gz | 4.1 KB | ||
Others | emd_25525_additional_1.map.gz emd_25525_half_map_1.map.gz emd_25525_half_map_2.map.gz | 7.3 MB 13.4 MB 13.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25525 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25525 | HTTPS FTP |
-Validation report
Summary document | emd_25525_validation.pdf.gz | 656.5 KB | Display | EMDB validaton report |
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Full document | emd_25525_full_validation.pdf.gz | 656.1 KB | Display | |
Data in XML | emd_25525_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_25525_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25525 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25525 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25525.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34564 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25525_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_25525_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_25525_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_25525_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : N-terminal half of P-Rex1 (PI(3,4,5)P3-dependent Rac Exchanger 1)
Entire | Name: N-terminal half of P-Rex1 (PI(3,4,5)P3-dependent Rac Exchanger 1) |
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Components |
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-Supramolecule #1: N-terminal half of P-Rex1 (PI(3,4,5)P3-dependent Rac Exchanger 1)
Supramolecule | Name: N-terminal half of P-Rex1 (PI(3,4,5)P3-dependent Rac Exchanger 1) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 191 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.18 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |