+Open data
-Basic information
Entry | Database: PDB / ID: 3qw9 | |||||||||
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Title | Crystal structure of betaglycan ZP-C domain | |||||||||
Components | Transforming growth factor beta receptor type 3 | |||||||||
Keywords | CYTOKINE RECEPTOR / immunoglobulin domain / Zona Pellucida / TGF-beta ligand co-receptor / protein polymerization | |||||||||
Function / homology | Function and homology information TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex ...TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex / definitive erythrocyte differentiation / muscular septum morphogenesis / response to follicle-stimulating hormone / response to prostaglandin E / BMP binding / vasculogenesis involved in coronary vascular morphogenesis / Signaling by Activin / apoptotic process involved in morphogenesis / secondary palate development / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / collagen metabolic process / negative regulation of epithelial cell migration / regulation of transforming growth factor beta receptor signaling pathway / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor binding / negative regulation of epithelial to mesenchymal transition / type II transforming growth factor beta receptor binding / heart trabecula morphogenesis / activin binding / heart trabecula formation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / transforming growth factor beta binding / definitive hemopoiesis / negative regulation of extracellular matrix assembly / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of SMAD protein signal transduction / ventricular septum morphogenesis / roof of mouth development / fibroblast growth factor binding / blood vessel development / outflow tract morphogenesis / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / blastocyst development / epithelial to mesenchymal transition / blood vessel remodeling / vasculogenesis / BMP signaling pathway / animal organ regeneration / coreceptor activity / positive regulation of cardiac muscle cell proliferation / negative regulation of canonical NF-kappaB signal transduction / transforming growth factor beta receptor signaling pathway / liver development / PDZ domain binding / negative regulation of transforming growth factor beta receptor signaling pathway / osteoblast differentiation / negative regulation of epithelial cell proliferation / cell migration / heparin binding / collagen-containing extracellular matrix / protein-containing complex assembly / cell population proliferation / in utero embryonic development / response to hypoxia / receptor complex / intracellular signal transduction / immune response / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / extracellular space / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å | |||||||||
Authors | Lin, S.J. / Jardetzky, T.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structure of betaglycan zona pellucida (ZP)-C domain provides insights into ZP-mediated protein polymerization and TGF-{beta} binding. Authors: Lin, S.J. / Hu, Y. / Zhu, J. / Woodruff, T.K. / Jardetzky, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qw9.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qw9.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qw9 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qw9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20078.031 Da / Num. of mol.: 2 / Fragment: unp residues 591-763 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tgfbr3 / Plasmid: pBACgus-3 / Cell line (production host): High5 / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: P26342 #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16-18% PEG 6000, 0.1 M Citrate, 0.9-1.0M LiCl2, pH 5.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 6.5 % / Av σ(I) over netI: 31.98 / Number: 207054 / Rmerge(I) obs: 0.148 / Χ2: 2.67 / D res high: 1.84 Å / D res low: 50 Å / Num. obs: 31736 / % possible obs: 98.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.84→50 Å / Num. obs: 31736 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.076 / Χ2: 2.669 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MIRAS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing set |
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Phasing MIR | Resolution: 1.73→47.71 Å / FOM acentric: 0.171 / FOM centric: 0.245 / Reflection acentric: 31955 / Reflection centric: 3670 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MIR der | Native set-ID: 1 / Resolution: 1.73→47.71 Å
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Phasing MIR der shell |
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