+Open data
-Basic information
Entry | Database: PDB / ID: 2jyv | ||||||
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Title | Human Granulin F | ||||||
Components | Granulin-2 | ||||||
Keywords | CYTOKINE / Granulin C / epithelin / human / stack of hairpins / Alternative splicing / Glycoprotein / Polymorphism / Secreted | ||||||
Function / homology | Function and homology information positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response ...positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response / lysosomal transport / lysosome organization / positive regulation of axon regeneration / negative regulation of respiratory burst involved in inflammatory response / positive regulation of endothelial cell migration / cytokine activity / positive regulation of epithelial cell proliferation / growth factor activity / trans-Golgi network / positive regulation of neuron apoptotic process / positive regulation of angiogenesis / azurophil granule lumen / late endosome / regulation of inflammatory response / protein-folding chaperone binding / negative regulation of neuron apoptotic process / lysosome / protein stabilization / endosome / positive regulation of cell migration / lysosomal membrane / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / signal transduction / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Tolkatchev, D. / Wang, P. / Chen, Z. / Xu, P. / Ni, F. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Structure dissection of human progranulin identifies well-folded granulin/epithelin modules with unique functional activities. Authors: Tolkatchev, D. / Malik, S. / Vinogradova, A. / Wang, P. / Chen, Z. / Xu, P. / Bennett, H.P. / Bateman, A. / Ni, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jyv.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jyv.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/2jyv ftp://data.pdbj.org/pub/pdb/validation_reports/jy/2jyv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7978.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRN / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: P28799 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 10 |