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Yorodumi- PDB-4nc3: Crystal structure of the 5-HT2B receptor solved using serial femt... -
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-Basic information
Entry | Database: PDB / ID: 4nc3 | ||||||
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Title | Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography in lipidic cubic phase. | ||||||
Components | Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562 | ||||||
Keywords | SIGNALING PROTEIN / ELECTRON TRANSPORT / Serial femtosecond crystallography / human 5HT2B receptor / ergotamine / novel protein engineering / GPCR Network / Membrane protein / lipidic cubic phase / PSI-Biology / free electron laser / Structural Genomics / GPCR / membrane | ||||||
Function / homology | Function and homology information behavior / intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / protein kinase C signaling / regulation of behavior / Serotonin receptors ...behavior / intestine smooth muscle contraction / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / protein kinase C signaling / regulation of behavior / Serotonin receptors / cellular response to temperature stimulus / embryonic morphogenesis / serotonin binding / G protein-coupled serotonin receptor activity / protein kinase C-activating G protein-coupled receptor signaling pathway / vasoconstriction / neurotransmitter receptor activity / G protein-coupled receptor internalization / cardiac muscle hypertrophy / neural crest cell differentiation / neural crest cell migration / cGMP-mediated signaling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of cell division / activation of phospholipase C activity / G-protein alpha-subunit binding / heart morphogenesis / release of sequestered calcium ion into cytosol / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / GTPase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of cytokine production / positive regulation of MAP kinase activity / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / iron ion binding / phosphorylation / dendrite / synapse / heme binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liu, W. / Wacker, D. / Gati, C. / Han, G.W. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Katritch, V. / Barty, A. ...Liu, W. / Wacker, D. / Gati, C. / Han, G.W. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Katritch, V. / Barty, A. / Zatsepin, N.A. / Li, D. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Seibert, M.M. / Wang, C. / Shah, S.T.A. / Basu, S. / Fromme, R. / Kupitz, C. / Rendek, K.N. / Grotjohann, I. / Fromme, P. / Kirian, R.A. / Beyerlein, K.R. / White, T.A. / Chapman, H.N. / Caffrey, M. / Spence, J.C.H. / Stevens, R.C. / Cherezov, V. / GPCR Network (GPCR) | ||||||
Citation | Journal: Science / Year: 2013 Title: Serial femtosecond crystallography of G protein-coupled receptors. Authors: Liu, W. / Wacker, D. / Gati, C. / Han, G.W. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Katritch, V. / Barty, A. / Zatsepin, N.A. / Li, D. / Messerschmidt, M. / Boutet, S. / ...Authors: Liu, W. / Wacker, D. / Gati, C. / Han, G.W. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Katritch, V. / Barty, A. / Zatsepin, N.A. / Li, D. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Seibert, M.M. / Wang, C. / Shah, S.T. / Basu, S. / Fromme, R. / Kupitz, C. / Rendek, K.N. / Grotjohann, I. / Fromme, P. / Kirian, R.A. / Beyerlein, K.R. / White, T.A. / Chapman, H.N. / Caffrey, M. / Spence, J.C. / Stevens, R.C. / Cherezov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nc3.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nc3.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/4nc3 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4nc3 | HTTPS FTP |
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-Related structure data
Related structure data | 4ib4S S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1169541 / Data set type: diffraction image data |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48283.273 Da / Num. of mol.: 1 / Fragment: BRIL / Mutation: M7W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: HTR2B, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P41595, UniProt: P0ABE7 |
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-Non-polymers , 9 types, 21 molecules
#2: Chemical | ChemComp-PLM / | ||||||||||
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#3: Chemical | ChemComp-ERM / | ||||||||||
#4: Chemical | ChemComp-CLR / | ||||||||||
#5: Chemical | ChemComp-OLC / ( #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-TRS / | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.48 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 100mM Tris/HCl pH8.0, 20-80mM MgCl2 and 30% (v/v) PEG400 , Lipidic Cubic Phase (LCP), temperature 293K |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
Detector | Type: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 1, 2013 / Details: K-B Mirrors |
Radiation | Monochromator: K-B Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35 Å / Num. obs: 16052 / % possible obs: 100 % / Redundancy: 1150 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IB4 Resolution: 2.8→34.681 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 31.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.681 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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