[English] 日本語
Yorodumi- PDB-5xez: Structure of the Full-length glucagon class B G protein-coupled r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xez | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Full-length glucagon class B G protein-coupled receptor | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / Human GCGR receptor / Class B / 7TM domain / membrane / LCP / XFEL | |||||||||
Function / homology | Function and homology information regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / cellular response to glucagon stimulus / exocytosis / peptide hormone binding / viral release from host cell by cytolysis / hormone-mediated signaling pathway / peptidoglycan catabolic process / cellular response to starvation ...regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / cellular response to glucagon stimulus / exocytosis / peptide hormone binding / viral release from host cell by cytolysis / hormone-mediated signaling pathway / peptidoglycan catabolic process / cellular response to starvation / response to nutrient / guanyl-nucleotide exchange factor activity / generation of precursor metabolites and energy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / regulation of blood pressure / Glucagon-type ligand receptors / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / endosome / defense response to bacterium / positive regulation of gene expression / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. ...Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T. / Sierra, R. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M. / Stevens, R. / Jiang, H. / Wang, M. / Zhao, Q. / Wu, B. | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Structure of the full-length glucagon class B G-protein-coupled receptor. Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / ...Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P.R. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M.A. / Stevens, R.C. / Zhao, Q. / Jiang, H. / Wang, M.W. / Wu, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xez.cif.gz | 731.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xez.ent.gz | 606 KB | Display | PDB format |
PDBx/mmJSON format | 5xez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xez_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xez_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5xez_validation.xml.gz | 65.6 KB | Display | |
Data in CIF | 5xez_validation.cif.gz | 89.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xez ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xez | HTTPS FTP |
-Related structure data
Related structure data | 5xf1C 4l6rS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
-Antibody , 2 types, 4 molecules CHDL
#2: Antibody | Mass: 24977.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23263.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
---|
-Protein / Non-polymers , 2 types, 4 molecules AB
#1: Protein | Mass: 65784.070 Da / Num. of mol.: 2 Fragment: UNP RESIDUES 27-256,UNP RESIDUES 2-161,UNP RESIDUES 260-432 Mutation: C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: GCGR, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47871, UniProt: D9IEF7, lysozyme #6: Chemical | |
---|
-Sugars , 2 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 73.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100mM HEPES, pH7.0, 300mM potassium phosphate monobasic, 25% PEG500DME, 100mM gly-gly-glycine |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å | |||||||||||||||
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 20, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 67598 / % possible obs: 100 % / Redundancy: 198 % / Net I/σ(I): 4.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L6R Resolution: 3→31.78 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.114 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→31.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|