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Open data
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Basic information
Entry | Database: PDB / ID: 5x6v | ||||||
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Title | Crystal structure of human heteroheptameric complex | ||||||
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![]() | PROTEIN BINDING / Ragulator Rag GTPase complex / scaffold / roadblock / lysosome / mTOR signaling / cell growth | ||||||
Function / homology | ![]() Ragulator complex => GO:0071986 / Energy dependent regulation of mTOR by LKB1-AMPK / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / Amino acids regulate mTORC1 / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex ...Ragulator complex => GO:0071986 / Energy dependent regulation of mTOR by LKB1-AMPK / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / Amino acids regulate mTORC1 / 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 / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / 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 / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / 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 / positive regulation of TOR signaling / regulation of receptor recycling / 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 / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / regulation of autophagy / 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 / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / GTP binding / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. ...Yonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. / Yamashita, E. / Nakagawa, A. / Okada, M. | ||||||
![]() | ![]() Title: Structural basis for the assembly of the Ragulator-Rag GTPase complex. Authors: Yonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. / Yamashita, E. / Nakagawa, A. / Okada, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.7 KB | Display | ![]() |
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PDB format | ![]() | 264.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.8 KB | Display | ![]() |
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Full document | ![]() | 498.5 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x6uSC ![]() 4arzS S: Starting model for refinement C: citing same article ( |
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Similar 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: 13868.886 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13517.450 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: 13405.055 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-161 / Mutation: S98E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules FG
#6: Protein | Mass: 15661.119 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 183-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#7: Protein | Mass: 15764.174 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 238-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 350 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-NA / |
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#9: Chemical | ChemComp-ACT / |
#10: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, ammonium acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: CCD / Date: Oct 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→125.45 Å / Num. obs: 57406 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 40.11 Å2 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.02→2.06 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X6U, 4ARZ Resolution: 2.02→20.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.164
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Displacement parameters | Biso mean: 59.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.02→20.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.07 Å / Total num. of bins used: 20
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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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