+
Open data
-
Basic information
Entry | Database: PDB / ID: 7upi | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex | ||||||
![]() |
| ||||||
![]() | CELL CYCLE / shoc2 / leucine-rich repeat / MRAs / protein phosphatase / RAS signaling / MAPK | ||||||
Function / homology | ![]() cellular response to growth hormone stimulus / protein phosphatase type 1 complex / regulation of glycogen catabolic process / negative regulation of neural precursor cell proliferation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / GTP-dependent protein binding / cyclic-GMP-AMP transmembrane import across plasma membrane / nerve growth factor signaling pathway ...cellular response to growth hormone stimulus / protein phosphatase type 1 complex / regulation of glycogen catabolic process / negative regulation of neural precursor cell proliferation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / GTP-dependent protein binding / cyclic-GMP-AMP transmembrane import across plasma membrane / nerve growth factor signaling pathway / protein phosphatase regulator activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of Ras protein signal transduction / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / negative regulation of neuron differentiation / fibroblast growth factor receptor signaling pathway / ribonucleoprotein complex binding / dephosphorylation / positive regulation of neuron differentiation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / small monomeric GTPase / G protein activity / cellular response to leukemia inhibitory factor / adherens junction / response to lead ion / RAF activation / lung development / circadian regulation of gene expression / regulation of circadian rhythm / positive regulation of neuron projection development / GDP binding / Circadian Clock / presynapse / actin cytoskeleton organization / perikaryon / protein phosphatase binding / Ras protein signal transduction / dendritic spine / cell cycle / cell division / GTPase activity / glutamatergic synapse / nucleolus / GTP binding / signal transduction / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
![]() | Fuller, J.R. / Hajian, B. / Lemke, C. / Kwon, J. / Bian, Y. / Aguirre, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-function analysis of the SHOC2-MRAS-PP1C holophosphatase complex. Authors: Jason J Kwon / Behnoush Hajian / Yuemin Bian / Lucy C Young / Alvaro J Amor / James R Fuller / Cara V Fraley / Abbey M Sykes / Jonathan So / Joshua Pan / Laura Baker / Sun Joo Lee / Douglas ...Authors: Jason J Kwon / Behnoush Hajian / Yuemin Bian / Lucy C Young / Alvaro J Amor / James R Fuller / Cara V Fraley / Abbey M Sykes / Jonathan So / Joshua Pan / Laura Baker / Sun Joo Lee / Douglas B Wheeler / David L Mayhew / Nicole S Persky / Xiaoping Yang / David E Root / Anthony M Barsotti / Andrew W Stamford / Charles K Perry / Alex Burgin / Frank McCormick / Christopher T Lemke / William C Hahn / Andrew J Aguirre / ![]() Abstract: Receptor tyrosine kinase (RTK)-RAS signalling through the downstream mitogen-activated protein kinase (MAPK) cascade regulates cell proliferation and survival. The SHOC2-MRAS-PP1C holophosphatase ...Receptor tyrosine kinase (RTK)-RAS signalling through the downstream mitogen-activated protein kinase (MAPK) cascade regulates cell proliferation and survival. The SHOC2-MRAS-PP1C holophosphatase complex functions as a key regulator of RTK-RAS signalling by removing an inhibitory phosphorylation event on the RAF family of proteins to potentiate MAPK signalling. SHOC2 forms a ternary complex with MRAS and PP1C, and human germline gain-of-function mutations in this complex result in congenital RASopathy syndromes. However, the structure and assembly of this complex are poorly understood. Here we use cryo-electron microscopy to resolve the structure of the SHOC2-MRAS-PP1C complex. We define the biophysical principles of holoenzyme interactions, elucidate the assembly order of the complex, and systematically interrogate the functional consequence of nearly all of the possible missense variants of SHOC2 through deep mutational scanning. We show that SHOC2 binds PP1C and MRAS through the concave surface of the leucine-rich repeat region and further engages PP1C through the N-terminal disordered region that contains a cryptic RVXF motif. Complex formation is initially mediated by interactions between SHOC2 and PP1C and is stabilized by the binding of GTP-loaded MRAS. These observations explain how mutant versions of SHOC2 in RASopathies and cancer stabilize the interactions of complex members to enhance holophosphatase activity. Together, this integrative structure-function model comprehensively defines key binding interactions within the SHOC2-MRAS-PP1C holophosphatase complex and will inform therapeutic development . | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 225.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 159.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 59.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26667MC ![]() 7t7aC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 20894.898 Da / Num. of mol.: 1 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 37615.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P62136, protein-serine/threonine phosphatase |
#3: Protein | Mass: 65029.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 5 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
#4: Chemical | ChemComp-GTP / | ||
---|---|---|---|
#5: Chemical | ChemComp-MG / | ||
#6: Chemical | #7: Chemical | ChemComp-CL / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: SHOC2-PP1C-MRAS holophosphatase / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) |
| |||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: Fluorinated octyl maltoside added immediately prior to vitrification | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 2.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Gatan Solarus using ambient air with power set to 20 watts Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 290 nm / Calibrated defocus max: 2840 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4721 Details: Movies were recorded in CDS + super-resolution mode, fractionating 60 e-/A2 over 52 movie frames |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 449384 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE |