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Yorodumi- PDB-7txh: Human MRas Q71R in complex with human Shoc2 LRR domain M173I and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7txh | ||||||
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Title | Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca | ||||||
Components |
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Keywords | HYDROLASE / RAS / PP1 / SHOC2 / LRR | ||||||
Function / homology | Function and homology information 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 / nerve growth factor signaling pathway / protein phosphatase 1 binding / protein phosphatase regulator activity ...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 / nerve growth factor signaling pathway / protein phosphatase 1 binding / protein phosphatase regulator activity / cadherin binding involved in cell-cell adhesion / GTP-dependent protein binding / 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 / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / 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 / cellular response to leukemia inhibitory factor / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / small monomeric GTPase / G protein activity / response to lead ion / adherens junction / lung development / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / positive regulation of neuron projection development / GDP binding / Circadian Clock / presynapse / perikaryon / actin cytoskeleton organization / protein phosphatase binding / Ras protein signal transduction / dendritic spine / cell cycle / cell division / GTPase activity / glutamatergic synapse / GTP binding / nucleolus / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hauseman, Z.J. / Viscomi, J. / Dhembi, A. / Clark, K. / King, D.A. / Fodor, M. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2022 Title: Structure of the MRAS-SHOC2-PP1C phosphatase complex. Authors: Hauseman, Z.J. / Fodor, M. / Dhembi, A. / Viscomi, J. / Egli, D. / Bleu, M. / Katz, S. / Park, E. / Jang, D.M. / Porter, K.A. / Meili, F. / Guo, H. / Kerr, G. / Molle, S. / Velez-Vega, C. / ...Authors: Hauseman, Z.J. / Fodor, M. / Dhembi, A. / Viscomi, J. / Egli, D. / Bleu, M. / Katz, S. / Park, E. / Jang, D.M. / Porter, K.A. / Meili, F. / Guo, H. / Kerr, G. / Molle, S. / Velez-Vega, C. / Beyer, K.S. / Galli, G.G. / Maira, S.M. / Stams, T. / Clark, K. / Eck, M.J. / Tordella, L. / Thoma, C.R. / King, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7txh.cif.gz | 1022.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7txh.ent.gz | 688 KB | Display | PDB format |
PDBx/mmJSON format | 7txh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txh ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txh | HTTPS FTP |
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-Related structure data
Related structure data | 7tygC 1x1sS 6zk6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 20567.482 Da / Num. of mol.: 2 / Mutation: Q71R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14807, small monomeric GTPase #2: Protein | Mass: 56719.543 Da / Num. of mol.: 2 / Mutation: M173I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHOC2, KIAA0862 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UQ13 #3: Protein | Mass: 33963.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli) References: UniProt: P62136, protein-serine/threonine phosphatase |
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-Non-polymers , 6 types, 1743 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-MN / #8: Chemical | ChemComp-PO4 / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M NaH2PO4 pH 6.5, 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→88.033 Å / Num. obs: 163294 / % possible obs: 99.86 % / Redundancy: 2 % / Biso Wilson estimate: 31.52 Å2 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.088 / Net I/σ(I): 10.49 |
Reflection shell | Resolution: 1.951→1.958 Å / Redundancy: 4.4 % / Num. unique obs: 1654 / CC1/2: 0.804 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZK6, 1X1S Resolution: 1.95→42.26 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5049 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→42.26 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.86067292567 Å / Origin y: 0.754078944801 Å / Origin z: 23.0618749266 Å
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Refinement TLS group | Selection details: all |