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- PDB-5tud: Structural Insights into the Extracellular Recognition of the Hum... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tud | |||||||||
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Title | Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody | |||||||||
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![]() | SIGNALING PROTEIN / 7-TM / GPCR / Fab / complex | |||||||||
Function / homology | ![]() 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 / embryonic morphogenesis / cellular response to temperature stimulus / serotonin binding / vasoconstriction / G protein-coupled serotonin receptor activity / : / G protein-coupled receptor internalization / cardiac muscle hypertrophy / neural crest cell differentiation / neural crest cell migration / neurotransmitter receptor activity / cGMP-mediated signaling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of cell division / : / G-protein alpha-subunit binding / heart morphogenesis / release of sequestered calcium ion into cytosol / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / calcium-mediated signaling / electron transport chain / positive regulation of MAP kinase activity / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / G protein-coupled receptor signaling pathway / phosphorylation / synapse / dendrite / heme binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ishchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Boutet, S. / James, D. / Wang, D. / Weierstall, U. ...Ishchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Boutet, S. / James, D. / Wang, D. / Weierstall, U. / Liu, W. / Katritch, V. / Stevens, R.C. / Cherezov, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody. Authors: Ishchenko, A. / Wacker, D. / Kapoor, M. / Zhang, A. / Han, G.W. / Basu, S. / Patel, N. / Messerschmidt, M. / Weierstall, U. / Liu, W. / Katritch, V. / Roth, B.L. / Stevens, R.C. / Cherezov, V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 636.1 KB | Display | ![]() |
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PDB format | ![]() | 527.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 71.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nc3S S: Starting model for refinement |
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Similar structure data |
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Links
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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: 51497.035 Da / Num. of mol.: 2 Fragment: UNP P41595 residues 36-248 and 314-405 linked by UNP P0ABE7 residues 23-128 Mutation: M144W, M1007W, H1102I, R1106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HTR2B, cybC / Plasmid: pFastBac / Production host: ![]() ![]() #2: Antibody | Mass: 23151.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 25483.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 64.21 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.7 Details: Tris/HCL pH 7.7, 60 mM Sodium/Potassium Tartrate, 25% PEG400. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jan 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.56 Å / Relative weight: 1 |
Reflection | Resolution: 3→35.64 Å / Num. obs: 48606 / % possible obs: 100 % / Redundancy: 310.3 % / Biso Wilson estimate: 90.32 Å2 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 120.26 % / Mean I/σ(I) obs: 0.4 / CC1/2: 0.34 / % possible all: 100 |
Serial crystallography measurement | Photons per pulse: 390000000000 Tphotons/pulse / Pulse duration: 35 fsec. / Pulse photon energy: 7.95 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Injector diameter: 1.5 µm |
Serial crystallography data reduction | Frames failed index: 193328 / Frames indexed: 52291 / Frames total: 1877040 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4NC3 Resolution: 3→35.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.896 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.822 / SU Rfree Blow DPI: 0.357 Details: unmodeled densities (potentially Zn ion) near (1) His232, His235 of chain C & Asp1 of chain E, and (2) His233, His231 of Chain C & His1063 of chain A
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Displacement parameters | Biso mean: 106.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.62 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→35.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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