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Yorodumi- PDB-6p7j: Crystal structure of Latency Associated Peptide unbound to TGF-beta1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p7j | ||||||
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Title | Crystal structure of Latency Associated Peptide unbound to TGF-beta1 | ||||||
Components | Transforming growth factor beta-1 proprotein | ||||||
Keywords | CYTOKINE / pro-domain / latency / cancer / transforming | ||||||
Function / homology | Function and homology information positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / connective tissue replacement involved in inflammatory response wound healing / positive regulation of receptor signaling pathway via STAT / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / positive regulation of extracellular matrix assembly / receptor catabolic process / negative regulation of extracellular matrix disassembly / TGFBR1 LBD Mutants in Cancer / type II transforming growth factor beta receptor binding / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / negative regulation of biomineral tissue development / cell-cell junction organization / negative regulation of myoblast differentiation / positive regulation of vascular permeability / deubiquitinase activator activity / positive regulation of endothelial cell apoptotic process / response to cholesterol / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / sprouting angiogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / negative regulation of fat cell differentiation / macrophage derived foam cell differentiation / Syndecan interactions / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / negative regulation of blood vessel endothelial cell migration / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / RUNX3 regulates p14-ARF / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / negative regulation of cell cycle / ECM proteoglycans / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / lymph node development / vasculogenesis / chondrocyte differentiation / hematopoietic progenitor cell differentiation / salivary gland morphogenesis / extrinsic apoptotic signaling pathway / regulation of cell migration / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / antigen binding / extracellular matrix / positive regulation of protein metabolic process / protein export from nucleus / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / positive regulation of superoxide anion generation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of miRNA transcription / negative regulation of protein phosphorylation / platelet alpha granule lumen / response to progesterone / cytokine activity / neural tube closure / positive regulation of protein secretion / positive regulation of protein-containing complex assembly Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.501 Å | ||||||
Authors | Stachowski, T.R. / Snell, M.E. / Snell, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Iucrj / Year: 2020 Title: Structural insights into conformational switching in latency-associated peptide between transforming growth factor beta-1 bound and unbound states Authors: Stachowski, T.R. / Snell, M.E. / Snell, E.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p7j.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p7j.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 6p7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7j ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7j | HTTPS FTP |
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-Related structure data
Related structure data | 5vqpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29274.240 Da / Num. of mol.: 1 / Mutation: R249A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Plasmid: pTT3 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01137 |
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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: 2.03 Å3/Da / Density % sol: 39.42 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4.6 Details: Reservoir composition: 20% PEG3350, 300 mM NaAc pH 4.6 |
-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 PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→36.31 Å / Num. obs: 3332 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.899 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.209 / Rrim(I) all: 0.406 / Net I/σ(I): 3.1 / Num. measured all: 12411 / Scaling rejects: 46 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VQP Resolution: 3.501→36.31 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / Phase error: 24.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||
Displacement parameters | Biso max: 224.46 Å2 / Biso mean: 111.1007 Å2 / Biso min: 40.77 Å2 | ||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.501→36.31 Å
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LS refinement shell | Resolution: 3.501→3.625 Å / Rfactor Rfree error: 0
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