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Yorodumi- PDB-1c28: THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c28 | ||||||
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Title | THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS AN EVOLUTIONARY LINK TO TUMOR NECROSIS FACTOR | ||||||
Components | PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30)) | ||||||
Keywords | SERUM PROTEIN / ACRP30 C1Q TNF TRIMER ALL-BETA | ||||||
Function / homology | Function and homology information AMPK inhibits chREBP transcriptional activation activity / negative regulation of intracellular protein transport / positive regulation of lipid transporter activity / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / response to linoleic acid / positive regulation of glycogen (starch) synthase activity / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process ...AMPK inhibits chREBP transcriptional activation activity / negative regulation of intracellular protein transport / positive regulation of lipid transporter activity / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / response to linoleic acid / positive regulation of glycogen (starch) synthase activity / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / negative regulation of macrophage differentiation / detection of oxidative stress / positive regulation of signal transduction / negative regulation of granulocyte differentiation / negative regulation of hormone secretion / low-density lipoprotein particle clearance / negative regulation of protein autophosphorylation / sialic acid binding / negative regulation of heterotypic cell-cell adhesion / response to sucrose / negative regulation of vascular associated smooth muscle cell migration / collagen trimer / negative regulation of DNA biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of monocyte chemotactic protein-1 production / negative regulation of synaptic transmission / positive regulation of cAMP-dependent protein kinase activity / negative regulation of phagocytosis / negative regulation of cold-induced thermogenesis / positive regulation of fatty acid metabolic process / fatty acid beta-oxidation / negative regulation of fat cell differentiation / positive regulation of protein kinase A signaling / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of macrophage derived foam cell differentiation / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / response to tumor necrosis factor / negative regulation of gluconeogenesis / response to glucose / brown fat cell differentiation / negative regulation of canonical NF-kappaB signal transduction / cellular response to cAMP / response to glucocorticoid / cellular response to epinephrine stimulus / negative regulation of blood pressure / protein serine/threonine kinase activator activity / negative regulation of cell migration / response to nutrient / response to activity / negative regulation of MAP kinase activity / negative regulation of receptor binding / protein localization to plasma membrane / cell periphery / positive regulation of interleukin-8 production / positive regulation of glucose import / response to bacterium / hormone activity / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / circadian rhythm / cellular response to insulin stimulus / glucose metabolic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / gene expression / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / response to hypoxia / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Shapiro, L. / Scherer, P. | ||||||
Citation | Journal: Curr.Biol. / Year: 1998 Title: The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor. Authors: Shapiro, L. / Scherer, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c28.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c28.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/1c28 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/1c28 | 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: 15626.402 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60994 #2: 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: 2.78 Å3/Da / Density % sol: 55.75 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.8% PEG 4K, 0.1M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4. ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. all: 29616 / Num. obs: 27888 / % possible obs: 92.82 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.05 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.199 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.8 Å2 |