+Open data
-Basic information
Entry | Database: PDB / ID: 6q2n | ||||||
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Title | Cryo-EM structure of RET/GFRa1/GDNF extracellular complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / RET / receptor tyrosine kinase / cryo-EM | ||||||
Function / homology | Function and homology information chemoattractant activity involved in axon guidance / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity ...chemoattractant activity involved in axon guidance / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity / glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / GDF15-GFRAL signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / : / regulation of morphogenesis of a branching structure / membrane protein proteolysis / regulation of dopamine uptake involved in synaptic transmission / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / neuron cell-cell adhesion / Formation of the nephric duct / enteric nervous system development / peristalsis / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of dopamine secretion / sympathetic nervous system development / peripheral nervous system development / innervation / organ induction / plasma membrane protein complex / regulation of stem cell differentiation / commissural neuron axon guidance / neuron maturation / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / NCAM1 interactions / mRNA stabilization / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / branching involved in ureteric bud morphogenesis / regulation of axonogenesis / extrinsic component of membrane / response to pain / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / transmembrane receptor protein tyrosine kinase activity / regulation of cell adhesion / embryonic organ development / cellular response to retinoic acid / NPAS4 regulates expression of target genes / multivesicular body / adult locomotory behavior / axon guidance / receptor protein-tyrosine kinase / positive regulation of cell differentiation / growth factor activity / receptor tyrosine kinase binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron projection development / MAPK cascade / neuron projection development / retina development in camera-type eye / regulation of gene expression / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / receptor complex / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / endosome membrane / early endosome / positive regulation of cell migration / response to xenobiotic stimulus / protein phosphorylation / external side of plasma membrane / axon / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / dendrite / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / Golgi apparatus / signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Li, J. / Shang, G.J. / Chen, Y.J. / Brautigam, C.A. / Liou, J. / Zhang, X.W. / Bai, X.C. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. Authors: Jie Li / Guijun Shang / Yu-Ju Chen / Chad A Brautigam / Jen Liou / Xuewu Zhang / Xiao-Chen Bai / Abstract: RET is a receptor tyrosine kinase (RTK) that plays essential roles in development and has been implicated in several human diseases. Different from most of RTKs, RET requires not only its cognate ...RET is a receptor tyrosine kinase (RTK) that plays essential roles in development and has been implicated in several human diseases. Different from most of RTKs, RET requires not only its cognate ligands but also co-receptors for activation, the mechanisms of which remain unclear due to lack of high-resolution structures of the ligand/co-receptor/receptor complexes. Here, we report cryo-EM structures of the extracellular region ternary complexes of GDF15/GFRAL/RET, GDNF/GFRα1/RET, NRTN/GFRα2/RET and ARTN/GFRα3/RET. These structures reveal that all the four ligand/co-receptor pairs, while using different atomic interactions, induce a specific dimerization mode of RET that is poised to bring the two kinase domains into close proximity for cross-phosphorylation. The NRTN/GFRα2/RET dimeric complex further pack into a tetrameric assembly, which is shown by our cell-based assays to regulate the endocytosis of RET. Our analyses therefore reveal both the common mechanism and diversification in the activation of RET by different ligands. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6q2n.cif.gz | 313 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q2n.ent.gz | 251.8 KB | Display | PDB format |
PDBx/mmJSON format | 6q2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q2n_validation.pdf.gz | 876.2 KB | Display | wwPDB validaton report |
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Full document | 6q2n_full_validation.pdf.gz | 900.1 KB | Display | |
Data in XML | 6q2n_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 6q2n_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/6q2n ftp://data.pdbj.org/pub/pdb/validation_reports/q2/6q2n | HTTPS FTP |
-Related structure data
Related structure data | 20575MC 6q2jC 6q2oC 6q2rC 6q2sC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 15096.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDNF / Production host: Escherichia coli (E. coli) / References: UniProt: P39905 #2: Protein | Mass: 46358.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFRA1, GDNFRA, RETL1, TRNR1 / Production host: Homo sapiens (human) / References: UniProt: P56159 #3: Protein | Mass: 69100.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RET, CDHF12, CDHR16, PTC, RET51 / Production host: Homo sapiens (human) References: UniProt: P07949, receptor protein-tyrosine kinase #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RET, GFRAL and GDF15 extracellular complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 200 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 46729 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 15 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37098 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | B value: 190 / Protocol: FLEXIBLE FIT / Space: REAL |