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- PDB-6ehr: The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ehr | ||||||
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Title | The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex | ||||||
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![]() | SIGNALING PROTEIN / Scaffolding complex / Rag-GTPases / mTOR / Ragulator / mTORC1 | ||||||
Function / homology | ![]() regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / regulation of TORC1 signaling ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / regulation of TORC1 signaling / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / enzyme-substrate adaptor activity / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / small GTPase-mediated signal transduction / lysosome organization / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / specific granule membrane / protein-membrane adaptor activity / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / viral genome replication / RNA splicing / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / positive regulation of protein localization to nucleus / GDP binding / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / glucose homeostasis / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / GTP binding / magnesium ion binding / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Scheffzek, K. / Naschberger, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling. Authors: de Araujo, M.E.G. / Naschberger, A. / Furnrohr, B.G. / Stasyk, T. / Dunzendorfer-Matt, T. / Lechner, S. / Welti, S. / Kremser, L. / Shivalingaiah, G. / Offterdinger, M. / Lindner, H.H. / ...Authors: de Araujo, M.E.G. / Naschberger, A. / Furnrohr, B.G. / Stasyk, T. / Dunzendorfer-Matt, T. / Lechner, S. / Welti, S. / Kremser, L. / Shivalingaiah, G. / Offterdinger, M. / Lindner, H.H. / Huber, L.A. / Scheffzek, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.1 KB | Display | ![]() |
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PDB format | ![]() | 267.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.1 KB | Display | ![]() |
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Full document | ![]() | 492.7 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Ragulator complex protein ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 13903.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13574.501 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 9622.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 10753.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 15828.839 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules FG
#6: Protein | Mass: 15287.651 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#7: Protein | Mass: 18171.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% [w/v] PEG 4000, 0.1M tri-sodium-citrate pH5.5, 5% [v/v] isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.898→46.224 Å / Num. obs: 21957 / % possible obs: 93.8 % / Redundancy: 4.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.078 / Rsym value: 0.176 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.9→3.07 Å / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.75 / Rpim(I) all: 0.478 / Rsym value: 1.049 / % possible all: 93.4 |
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Processing
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Refinement | Resolution: 2.898→46.224 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.898→46.224 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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