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Yorodumi- PDB-3qbq: Crystal structure of extracellular domains of mouse RANK-RANKL complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qbq | |||||||||
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Title | Crystal structure of extracellular domains of mouse RANK-RANKL complex | |||||||||
Components |
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Keywords | CYTOKINE/CYTOKINE RECEPTOR / tumor necrosis factor (TNF) Ligand-receptor superfamily fold / cytokine-cytokine receptor complex | |||||||||
Function / homology | Function and homology information multinuclear osteoclast differentiation / 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 / circadian temperature homeostasis / tumor necrosis factor receptor superfamily binding ...multinuclear osteoclast differentiation / 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 / circadian temperature homeostasis / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / TNFR2 non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / cellular response to zinc ion starvation / paracrine signaling / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / osteoclast development / mammary gland epithelial cell proliferation / cytokine binding / monocyte chemotaxis / mammary gland alveolus development / positive regulation of bone resorption / calcium ion homeostasis / response to tumor necrosis factor / lymph node development / response to mechanical stimulus / positive regulation of phosphorylation / JNK cascade / bone resorption / tumor necrosis factor-mediated signaling pathway / ERK1 and ERK2 cascade / response to interleukin-1 / ossification / phosphatidylinositol 3-kinase/protein kinase B signal transduction / osteoclast differentiation / cellular response to leukemia inhibitory factor / cytokine activity / calcium-mediated signaling / animal organ morphogenesis / positive regulation of JNK cascade / response to insulin / bone development / response to organic cyclic compound / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / adaptive immune response / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / immune response / membrane raft / external side of plasma membrane / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Ta, H.M. / Nguyen, G.T.T. / Jin, H.M. / Choi, J.K. / Park, H. / Kim, N.S. / Hwang, H.Y. / Kim, K.K. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structure-based development of a receptor activator of nuclear factor-kappaB ligand (RANKL) inhibitor peptide and molecular basis for osteopetrosis Authors: Ta, H.M. / Nguyen, G.T.T. / Jin, H.M. / Choi, J.K. / Park, H. / Kim, N.S. / Hwang, H.Y. / Kim, K.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qbq.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbq.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qbq_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 3qbq_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 3qbq_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 3qbq_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbq ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbq | HTTPS FTP |
-Related structure data
Related structure data | 1iqaS S: Starting model for refinement |
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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: 17860.000 Da / Num. of mol.: 2 / Fragment: residues 157-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rankl / Plasmid: pVFT3S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O35235 #2: Protein | Mass: 18669.074 Da / Num. of mol.: 2 / Fragment: residues 32-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rank / Plasmid: pVFT3S / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: O35305 #3: 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: 5.4 Å3/Da / Density % sol: 77.2 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 5.6 Details: 100mM trisodium citrate, 1.2M ammonium sulfate, pH 5.6, microbatch, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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Detector | Detector: CCD / Date: Jun 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.66 Å / Num. obs: 52575 / Redundancy: 10.46 % / Biso Wilson estimate: 52.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 31.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IQA Resolution: 2.5→45.66 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 1976536 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5049 Å2 / ksol: 0.3327 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.13 Å2 / Biso mean: 62.0759 Å2 / Biso min: 22.85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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