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- PDB-6gff: Structure of GARP (LRRC32) in complex with latent TGF-beta1 and M... -
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Basic information
Entry | Database: PDB / ID: 6gff | |||||||||
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Title | Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab | |||||||||
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![]() | IMMUNE SYSTEM / GARP / TGF-B1 / Activation / Treg | |||||||||
Function / homology | ![]() : / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / regulation of branching involved in mammary gland duct morphogenesis / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / frontal suture morphogenesis / negative regulation of skeletal muscle tissue development / regulation of enamel mineralization ...: / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / regulation of branching involved in mammary gland duct morphogenesis / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / frontal suture morphogenesis / negative regulation of skeletal muscle tissue development / regulation of enamel mineralization / regulatory T cell differentiation / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of blood vessel remodeling / tolerance induction to self antigen / regulation of striated muscle tissue development / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / columnar/cuboidal epithelial cell maturation / type III transforming growth factor beta receptor binding / positive regulation of odontogenesis / Langerhans cell differentiation / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / positive regulation of receptor signaling pathway via STAT / connective tissue replacement involved in inflammatory response wound healing / positive regulation of exit from mitosis / extracellular matrix assembly / negative regulation of macrophage cytokine production / odontoblast differentiation / : / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of isotype switching to IgA isotypes / secondary palate development / positive regulation of mesenchymal stem cell proliferation / mammary gland branching involved in thelarche / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / membrane protein intracellular domain proteolysis / heart valve morphogenesis / retina vasculature development in camera-type eye / response to laminar fluid shear stress / positive regulation of primary miRNA processing / positive regulation of vasculature development / bronchiole development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / oligodendrocyte development / germ cell migration / response to salt / negative regulation of biomineral tissue development / endoderm development / type I transforming growth factor beta receptor binding / positive regulation of chemotaxis / phospholipid homeostasis / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / positive regulation of endothelial cell apoptotic process / positive regulation of vascular permeability / response to vitamin D / cell-cell junction organization / positive regulation of regulatory T cell differentiation / transforming growth factor beta binding / response to cholesterol / digestive tract development / negative regulation of interleukin-17 production / surfactant homeostasis / deubiquitinase activator activity / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of ossification / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of fibroblast migration / aortic valve morphogenesis / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / negative regulation of phagocytosis / sprouting angiogenesis / face morphogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / negative regulation of cytokine production / ventricular cardiac muscle tissue morphogenesis / cellular response to insulin-like growth factor stimulus / ureteric bud development / positive regulation of epidermal growth factor receptor signaling pathway / macrophage derived foam cell differentiation / negative regulation of neuroblast proliferation / Syndecan interactions Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Merceron, R. / Lienart, S. / Vanderaa, C. / Colau, D. / Stockis, J. / Van Der Woning, B. / De Haard, H. / Saunders, M. / Coulie, P.G. / Savvides, S.N. / Lucas, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of latent TGF-beta 1 presentation and activation by GARP on human regulatory T cells. Authors: Lienart, S. / Merceron, R. / Vanderaa, C. / Lambert, F. / Colau, D. / Stockis, J. / van der Woning, B. / De Haard, H. / Saunders, M. / Coulie, P.G. / Savvides, S.N. / Lucas, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 928.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 94.2 KB | Display | |
Data in CIF | ![]() | 129.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Transforming growth factor beta- ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 28531.488 Da / Num. of mol.: 4 / Fragment: LAP Source method: isolated from a genetically manipulated source Details: Mature protein expected to start at Leucine30. Obtained after cleavage of Pro-TGF-b1 by Furin after Arginine278. Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 12809.812 Da / Num. of mol.: 4 / Fragment: Mature Source method: isolated from a genetically manipulated source Details: Obtained after cleavage of Pro-TGF-b1 by Furin after Arginine278. Source: (gene. exp.) ![]() ![]() |
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-Protein , 1 types, 2 molecules IJ
#3: Protein | Mass: 67235.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Mature protein expected to start at Histidine20. / Source: (gene. exp.) ![]() ![]() |
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-Antibody , 2 types, 4 molecules KMLN
#4: Antibody | Mass: 23376.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Mature protein expected to start at Aspartic acid21. Source: (natural) ![]() ![]() #5: Antibody | Mass: 23832.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mature protein expected to start at Glutamine20. / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 7 molecules
#6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG4000, 0.1 M HEPES pH 6.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 84967 / % possible obs: 90.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 77.7 Å2 / Net I/σ(I): 8.15 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 2.2 % / Num. unique obs: 6320 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→29.921 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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