+Open data
-Basic information
Entry | Database: PDB / ID: 6j21 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human NK1 substance P receptor | ||||||
Components | Substance-P receptor,Endolysin | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / Complex / Antagonist / signalling protein | ||||||
Function / homology | Function and homology information substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation ...substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation / operant conditioning / sperm head / sperm ejaculation / response to ozone / positive regulation of action potential / response to auditory stimulus / smooth muscle contraction involved in micturition / positive regulation of blood pressure / regulation of smooth muscle cell proliferation / positive regulation of hormone secretion / positive regulation of vascular permeability / positive regulation of ossification / regulation of smooth muscle cell migration / positive regulation of leukocyte migration / eating behavior / positive regulation of epithelial cell migration / behavioral response to pain / angiotensin-mediated drinking behavior / associative learning / sperm flagellum / long-term memory / response to electrical stimulus / positive regulation of vasoconstriction / viral release from host cell by cytolysis / positive regulation of stress fiber assembly / sperm midpiece / peptidoglycan catabolic process / response to progesterone / positive regulation of epithelial cell proliferation / positive regulation of synaptic transmission, GABAergic / response to nicotine / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / response to estradiol / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / lysozyme activity / cell body / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / response to ethanol / host cell cytoplasm / defense response to bacterium / inflammatory response / dendrite / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Chen, S. / Lu, M. / Zhang, H. / Wu, B. / Zhao, Q. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography. Authors: Chen, S. / Lu, M. / Liu, D. / Yang, L. / Yi, C. / Ma, L. / Zhang, H. / Liu, Q. / Frimurer, T.M. / Wang, M.W. / Schwartz, T.W. / Stevens, R.C. / Wu, B. / Wuthrich, K. / Zhao, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6j21.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6j21.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/6j21 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/6j21 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6j20C 4u15S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50428.781 Da / Num. of mol.: 1 / Mutation: E78N,Y121W,Q165A,T222R,C97A Source method: isolated from a genetically manipulated source Details: The fusion protein of Substance-P receptor NK1R (residues 2-226), mini-T4L (residues 1001-1010, 1017-1117), LINKER GGGSGG (residues 1011-1016), and NK1R (residues 237-335) Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: TACR1, NK1R, TAC1R, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25103, UniProt: D9IEF7, lysozyme |
---|---|
#2: Chemical | ChemComp-GBQ / |
#3: Chemical | ChemComp-OLC / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.49 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.1M MES, pH 6.0-6.6, 25-35% PEG 400, 200-350mM ammonium tartrate dibasic PH range: 6.0-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 13746 / % possible obs: 93.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 132.25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.2→3.46 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.77 / Num. unique obs: 2038 / CC1/2: 0.77 / % possible all: 97.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U15 Resolution: 3.2→29.98 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.217 / SU Rfree Blow DPI: 0.394 / SU Rfree Cruickshank DPI: 0.398
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→29.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 4.1682 Å / Origin y: 138.876 Å / Origin z: 188.105 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |