+Open data
-Basic information
Entry | Database: PDB / ID: 5vqf | |||||||||
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Title | Crystal Structure of pro-TGF-beta 1 | |||||||||
Components | Transforming growth factor beta-1 | |||||||||
Keywords | PROTEIN BINDING / pro-complex / latency / homodimer | |||||||||
Function / homology | Function and homology information Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity ...Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity / regulation of binding / regulation of DNA binding / positive regulation of microglia differentiation / negative regulation of skeletal muscle tissue development / regulation of striated muscle tissue development / regulation of protein import into nucleus / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / extracellular matrix assembly / negative regulation of macrophage cytokine production / odontoblast differentiation / positive regulation of isotype switching to IgA isotypes / membrane protein intracellular domain proteolysis / hyaluronan catabolic process / ATP biosynthetic process / receptor catabolic process / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / positive regulation of chemotaxis / negative regulation of myoblast differentiation / cell-cell junction organization / response to cholesterol / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of blood vessel endothelial cell migration / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of cell-cell adhesion / negative regulation of fat cell differentiation / salivary gland morphogenesis / positive regulation of interleukin-17 production / positive regulation of SMAD protein signal transduction / positive regulation of cell division / negative regulation of cell cycle / positive regulation of collagen biosynthetic process / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / lymph node development / chondrocyte differentiation / hematopoietic progenitor cell differentiation / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / positive regulation of superoxide anion generation / : / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / extracellular matrix / transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / cytokine activity / antigen binding / response to progesterone / positive regulation of protein secretion / growth factor activity / positive regulation of protein-containing complex assembly / negative regulation of cell growth / response to wounding / positive regulation of protein import into nucleus / negative regulation of epithelial cell proliferation / response to estradiol / regulation of cell population proliferation / positive regulation of ERK1 and ERK2 cascade / blood microparticle / positive regulation of cell migration / inflammatory response / protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Zhao, B. / Xu, S. / Dong, X. / Lu, C. / Springer, T.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Prodomain-growth factor swapping in the structure of pro-TGF-beta 1. Authors: Zhao, B. / Xu, S. / Dong, X. / Lu, C. / Springer, T.A. #1: Journal: Nature / Year: 2011 Title: Latent TGF-beta structure and activation. Authors: Shi, M. / Zhu, J. / Wang, R. / Chen, X. / Mi, L. / Walz, T. / Springer, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vqf.cif.gz | 564.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vqf.ent.gz | 473.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vqf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5vqf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5vqf_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 5vqf_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/5vqf ftp://data.pdbj.org/pub/pdb/validation_reports/vq/5vqf | HTTPS FTP |
-Related structure data
Related structure data | 5vqpC 3rjrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41432.410 Da / Num. of mol.: 4 / Mutation: C4S, N147Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: TGFB1 / Plasmid: pEF1-puro Details (production host): pEF1-puro is derived from pEF1/V5-HisA (Invitrogen) with the neomycin gene replaced with puromycin. Cell (production host): epithelial / Cell line (production host): CHO-lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Ovary / References: UniProt: P07200 #2: 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 #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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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: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 7% PEG 3350, 17% isopropanol, 0.1m Na citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934, 0.97932, 0.97956, 0.95667 | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2009 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→50 Å / Num. obs: 39918 / % possible obs: 96.1 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3 | |||||||||||||||
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.74 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 2994 / CC1/2: 0.33 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RJR Resolution: 2.9→37.142 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→37.142 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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