+Open data
-Basic information
Entry | Database: PDB / ID: 5yk5 | ||||||
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Title | structure of the human Lamtor4-Lamtor5 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / cellular signal transduction pathway | ||||||
Function / homology | Function and homology information positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy ...positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy / mTORC1-mediated signalling / positive regulation of TOR signaling / positive regulation of TORC1 signaling / viral genome replication / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein localization to nucleus / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Wu, G. / Mu, Z. | ||||||
Citation | Journal: Cell Discov / Year: 2017 Title: Structural insight into the Ragulator complex which anchors mTORC1 to the lysosomal membrane Authors: Mu, Z. / Wang, L. / Deng, W. / Wang, J. / Wu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yk5.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yk5.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yk5_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 5yk5_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 5yk5_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5yk5_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yk5 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yk5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 9195.485 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1 |
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#2: Protein | Mass: 9346.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504 |
#3: Protein | Mass: 9051.334 Da / Num. of mol.: 1 / Mutation: E10A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1 |
#4: Protein | Mass: 9133.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, pH 8.0, 3.5M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 22500 / % possible obs: 100 % / Redundancy: 10.3 % / Net I/σ(I): 20.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 14.694 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.59 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→50 Å
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Refine LS restraints |
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