[English] 日本語
Yorodumi- PDB-6gff: Structure of GARP (LRRC32) in complex with latent TGF-beta1 and M... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 6gff | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / GARP / TGF-B1 / Activation / Treg | |||||||||
| Function / homology | Function and homology informationestablishment of protein localization to extracellular region / cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation ...establishment of protein localization to extracellular region / cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development / embryonic liver development / macrophage derived foam cell differentiation / response to laminar fluid shear stress / regulation of enamel mineralization / regulation of branching involved in mammary gland duct morphogenesis / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulation of blood vessel remodeling / regulation of protein import into nucleus / regulatory T cell differentiation / tolerance induction to self antigen / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / myofibroblast differentiation / positive regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / secondary palate development / negative regulation of macrophage cytokine production / odontoblast differentiation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / heart valve morphogenesis / bronchiole development / TGFBR3 regulates TGF-beta signaling / mammary gland branching involved in thelarche / hyaluronan catabolic process / positive regulation of vasculature development / lens fiber cell differentiation / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of chemotaxis / TGFBR1 LBD Mutants in Cancer / receptor ligand inhibitor activity / type I transforming growth factor beta receptor binding / positive regulation of mononuclear cell migration / response to salt / germ cell migration / endoderm development / negative regulation of biomineral tissue development / phospholipid homeostasis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / positive regulation of vascular permeability / response to cholesterol / oligodendrocyte development / cell-cell junction organization / negative regulation of interleukin-17 production / phosphate-containing compound metabolic process / surfactant homeostasis / transforming growth factor beta binding / deubiquitinase activator activity / sprouting angiogenesis / 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 / digestive tract development / aortic valve morphogenesis / RUNX3 regulates CDKN1A transcription / response to vitamin D / face morphogenesis / positive regulation of fibroblast migration / ureteric bud development / neural tube development / positive regulation of regulatory T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / Molecules associated with elastic fibres / negative regulation of phagocytosis / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of neuroblast proliferation / negative regulation of cytokine production / lung alveolus development / Syndecan interactions Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human)![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | 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 | Belgium, 2items
| |||||||||
Citation | Journal: Science / Year: 2018Title: 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 |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 6gff.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb6gff.ent.gz | 928.2 KB | Display | PDB format |
| PDBx/mmJSON format | 6gff.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6gff_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 6gff_full_validation.pdf.gz | 2.3 MB | Display | |
| Data in XML | 6gff_validation.xml.gz | 108 KB | Display | |
| Data in CIF | 6gff_validation.cif.gz | 139.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/6gff ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gff | HTTPS FTP |
-Related structure data
| Similar structure data |
|---|
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||
| 2 | ![]()
| ||||||||
| Unit cell |
|
-
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.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137#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.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137 |
|---|
-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.) Homo sapiens (human) / Gene: LRRC32, D11S833E, GARP / Production host: Homo sapiens (human) / References: UniProt: Q14392 |
|---|
-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) ![]() |
|---|
-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 |
|---|
-Details
| Has protein modification | Y |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.67 % |
|---|---|
| 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 |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
| 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 |
-
Processing
| Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.921 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.07
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.1→29.921 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement TLS group |
|
Movie
Controller
About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
Belgium, 2items
Citation





PDBj





















