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Yorodumi- EMDB-2712: Structure of the RET receptor tyrosine kinase extracellular domain -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2712 | |||||||||
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Title | Structure of the RET receptor tyrosine kinase extracellular domain | |||||||||
Map data | Reconstruction of a reconstituted mammalian RETecd-GDNF-GFRa1 ternary (mTC) complex | |||||||||
Sample |
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Keywords | vertebrate development / human diseases / RET-GFL-GFRa complex | |||||||||
Function / homology | Function and homology information chemoattractant activity involved in axon guidance / postsynaptic membrane organization / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / 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 / postsynaptic membrane organization / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / 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 / RET signaling / 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 / regulation of dopamine uptake involved in synaptic transmission / membrane protein proteolysis / neurotrophin receptor activity / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / Formation of the nephric duct / enteric nervous system development / neuron cell-cell adhesion / peristalsis / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of dopamine secretion / sympathetic nervous system development / innervation / peripheral nervous system development / organ induction / regulation of stem cell differentiation / plasma membrane protein complex / metanephros development / commissural neuron axon guidance / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / mRNA stabilization / NCAM1 interactions / RAF/MAP kinase cascade / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / branching involved in ureteric bud morphogenesis / response to pain / regulation of axonogenesis / 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 / embryonic organ development / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / multivesicular body / adult locomotory behavior / kidney development / positive regulation of cell differentiation / axon guidance / growth factor activity / neuron differentiation / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / positive regulation of neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / MAPK cascade / cell migration / integrin binding / retina development in camera-type eye / nervous system development / signaling receptor activity / RAF/MAP kinase cascade / regulation of gene expression / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / external side of plasma membrane / axon / protein phosphorylation / signaling receptor binding / neuronal cell body / calcium ion binding / dendrite Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
Authors | Goodman K / Kjaer S / Beuron F / Knowles P / Nawrotek A / Burns E / Purkiss A / George R / Santoro M / Morris EP / McDonald NQ | |||||||||
Citation | Journal: Cell Rep / Year: 2014 Title: RET recognition of GDNF-GFRα1 ligand by a composite binding site promotes membrane-proximal self-association. Authors: Kerry M Goodman / Svend Kjær / Fabienne Beuron / Phillip P Knowles / Agata Nawrotek / Emily M Burns / Andrew G Purkiss / Roger George / Massimo Santoro / Edward P Morris / Neil Q McDonald / Abstract: The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a ...The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a GFRα coreceptor, resulting in RET transmembrane signaling. We present a hybrid structural model, derived from electron microscopy (EM) and low-angle X-ray scattering (SAXS) data, of the RET extracellular domain (RET(ECD)), GDNF, and GFRα1 ternary complex, defining the basis for ligand recognition. RET(ECD) envelopes the dimeric ligand complex through a composite binding site comprising four discrete contact sites. The GFRα1-mediated contacts are crucial, particularly close to the invariant RET calcium-binding site, whereas few direct contacts are made by GDNF, explaining how distinct ligand/coreceptor pairs are accommodated. The RET(ECD) cysteine-rich domain (CRD) contacts both ligand components and makes homotypic membrane-proximal interactions occluding three different antibody epitopes. Coupling of these CRD-mediated interactions suggests models for ligand-induced RET activation and ligand-independent oncogenic deregulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2712.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-2712-v30.xml emd-2712.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | EMD-2712.png | 71.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2712 | HTTPS FTP |
-Validation report
Summary document | emd_2712_validation.pdf.gz | 202.2 KB | Display | EMDB validaton report |
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Full document | emd_2712_full_validation.pdf.gz | 201.3 KB | Display | |
Data in XML | emd_2712_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2712 | HTTPS FTP |
-Related structure data
Related structure data | 4ux8MC 2713C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2712.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of a reconstituted mammalian RETecd-GDNF-GFRa1 ternary (mTC) complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Reconstituted mammalian RETecd-GDNF-GFRa1 ternary complex
Entire | Name: Reconstituted mammalian RETecd-GDNF-GFRa1 ternary complex |
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Components |
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-Supramolecule #1000: Reconstituted mammalian RETecd-GDNF-GFRa1 ternary complex
Supramolecule | Name: Reconstituted mammalian RETecd-GDNF-GFRa1 ternary complex type: sample / ID: 1000 Details: Monodisperse. Measured mass difference with theoretical MW corresponds to glycosylation. Oligomeric state: Hexamer / Number unique components: 3 |
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Molecular weight | Experimental: 340 KDa / Theoretical: 260 KDa / Method: SEC-MALS |
-Macromolecule #1: RET receptor tyrosine kinase
Macromolecule | Name: RET receptor tyrosine kinase / type: protein_or_peptide / ID: 1 / Name.synonym: RET / Number of copies: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 80 KDa |
Recombinant expression | Organism: Chinese Hamster Ovary (Chinese hamster) / Recombinant strain: Lec8 |
-Macromolecule #2: GDNF receptor alpha
Macromolecule | Name: GDNF receptor alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: rat |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Chinese Hamster Ovary (Chinese hamster) |
-Macromolecule #3: glial-cell-line-derived neurotrophic factor
Macromolecule | Name: glial-cell-line-derived neurotrophic factor / type: protein_or_peptide / ID: 3 / Name.synonym: GDNF / Details: from Amgen (USA) / Number of copies: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 10 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 8 / Details: 20 mM Tris HCl, 300 mM NaCl, 1 mM Ca++ |
Staining | Type: NEGATIVE Details: Samples were applied to glow-discharged grids and stained with 2% uranyl acetate |
Grid | Details: quantifoil (R1.2/1.3) coated with a thin carbon layer, glow discharge in air. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Nov 8, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 1200 / Average electron dose: 100 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.9 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected manually. The starting model was calculated from reference-free classes using angular reconstitution methods and further refined by projection matching. |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: IMAGIC, SPIDER, in-house, software / Number images used: 8519 |
Final two d classification | Number classes: 975 |