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Yorodumi- PDB-4iaq: Crystal structure of the chimeric protein of 5-HT1B-BRIL in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iaq | ||||||
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Title | Crystal structure of the chimeric protein of 5-HT1B-BRIL in complex with dihydroergotamine (PSI Community Target) | ||||||
Components | Chimera protein of human 5-hydroxytryptamine receptor 1B and E. Coli soluble cytochrome b562 | ||||||
Keywords | Signaling Protein / Electron Transport / dihydroergotamine / Novel protein engineering / GPCR Network / Membrane protein / PSI-Biology / Structural Genomics / GPCR / GPCR Dock | ||||||
Function / homology | Function and homology information voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of gamma-aminobutyric acid secretion / G protein-coupled serotonin receptor complex / serotonergic synapse / regulation of behavior / Serotonin receptors / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of gamma-aminobutyric acid secretion / G protein-coupled serotonin receptor complex / serotonergic synapse / regulation of behavior / Serotonin receptors / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / drinking behavior / cellular response to temperature stimulus / serotonin binding / bone remodeling / negative regulation of synaptic transmission, glutamatergic / 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 / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / cellular response to alkaloid / heterocyclic compound binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / calyx of Held / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / response to cocaine / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / response to ethanol / electron transfer activity / periplasmic space / iron ion binding / dendrite / heme binding / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X. / Vardy, E. ...Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, E.X. / Melcher, K. / Zhang, C. / Bai, F. / Yang, H. / Yang, L. / Jiang, H. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / Xu, H.E. / GPCR Network (GPCR) | ||||||
Citation | Journal: Science / Year: 2013 Title: Structural basis for molecular recognition at serotonin receptors. Authors: Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X.P. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, X.E. / Melcher, K. / Zhang, C. / Bai, F. ...Authors: Wang, C. / Jiang, Y. / Ma, J. / Wu, H. / Wacker, D. / Katritch, V. / Han, G.W. / Liu, W. / Huang, X.P. / Vardy, E. / McCorvy, J.D. / Gao, X. / Zhou, X.E. / Melcher, K. / Zhang, C. / Bai, F. / Yang, H. / Yang, L. / Jiang, H. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iaq.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iaq.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 4iaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/4iaq ftp://data.pdbj.org/pub/pdb/validation_reports/ia/4iaq | HTTPS FTP |
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-Related structure data
Related structure data | 4iarC 4eiyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 45517.031 Da / Num. of mol.: 1 / Mutation: L138W, M29W, H124I, R128L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: 5HT1B_HUMAN, HTR1B, HTR1DB, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P28222, UniProt: P0ABE7 |
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#2: Chemical | ChemComp-2GM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 56 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.08 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8.7 Details: 100 mM Tris pH 8.7, 32-36% (v/v) PEG400, 90 mM sodium citrate tribasic dihydrate, 120 mM ammonium sulfate , Lipid Cubic Phase (LCP), temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 14244 / % possible obs: 92.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 79.31 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 24.2 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.4 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EIY Resolution: 2.8→35.06 Å / Cor.coef. Fo:Fc: 0.9159 / Cor.coef. Fo:Fc free: 0.8941 / SU R Cruickshank DPI: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 97.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.578 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→35.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→3.02 Å / Total num. of bins used: 7
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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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