+Open data
-Basic information
Entry | Database: PDB / ID: 4e4d | ||||||
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Title | Crystal structure of mouse RANKL-OPG complex | ||||||
Components |
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Keywords | Cytokine/Signaling Protein / TNF-Related Activation-Induced Cytokine-Receptor / Cysteine-Rich Domain / Jelly-Roll Fold / Cytokine-Signaling Protein complex | ||||||
Function / homology | Function and homology information negative regulation of odontogenesis of dentin-containing tooth / positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / : / tooth eruption / positive regulation of osteoclast development / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / : / TNFs bind their physiological receptors ...negative regulation of odontogenesis of dentin-containing tooth / positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / : / tooth eruption / positive regulation of osteoclast development / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / : / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / TNFR2 non-canonical NF-kB pathway / response to xenobiotic stimulus => GO:0009410 / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / paracrine signaling / response to arsenic-containing substance / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / negative regulation of bone resorption / osteoclast development / positive regulation of intracellular signal transduction / mammary gland epithelial cell proliferation / monocyte chemotaxis / response to magnesium ion / mammary gland alveolus development / positive regulation of bone resorption / calcium ion homeostasis / lymph node development / JNK cascade / positive regulation of phosphorylation / bone resorption / ERK1 and ERK2 cascade / tumor necrosis factor-mediated signaling pathway / extracellular matrix / ossification / extracellular matrix organization / osteoclast differentiation / response to nutrient / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to leukemia inhibitory factor / canonical NF-kappaB signal transduction / cytokine activity / calcium-mediated signaling / positive regulation of JNK cascade / animal organ morphogenesis / bone development / cytokine-mediated signaling pathway / response to estrogen / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / apoptotic process / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Nelson, C.A. / Fremont, D.H. | ||||||
Citation | Journal: Structure / Year: 2012 Title: RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor. Authors: Nelson, C.A. / Warren, J.T. / Wang, M.W. / Teitelbaum, S.L. / Fremont, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e4d.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e4d.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 4e4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/4e4d ftp://data.pdbj.org/pub/pdb/validation_reports/e4/4e4d | HTTPS FTP |
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-Related structure data
Related structure data | 4giqC 1jtzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17376.463 Da / Num. of mol.: 1 / Fragment: UNP residues 162-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CD254, ODF, Opgl, Rankl, Tnfsf11, Trance / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)-RIL / References: UniProt: O35235 | ||
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#2: Protein | Mass: 20372.166 Da / Num. of mol.: 1 / Fragment: UNP residues 22-197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 B / Gene: Ocif, Opg, Osteoprotegerin, Tnfrsf11b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HIGH FIVE / References: UniProt: O08712 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 100 mM sodium phosphate/citrate buffer, 14% polyethylene glycol 8000 and 250 mM sodium chloride, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9951 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 1, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9951 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 14915 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 48.42 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JTZ Resolution: 2.7→40.7 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Phase error: 23.59 / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→40.7 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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