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Yorodumi- EMDB-20572: Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20572 | |||||||||
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Title | Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 | |||||||||
Map data | Cryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement. | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / lymphocyte migration into lymphoid organs ...negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of neuron maturation / neuron cell-cell adhesion / enteric nervous system development / innervation / plasma membrane protein complex / neuron maturation / SMAD protein signal transduction / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / response to pain / negative regulation of multicellular organism growth / regulation of axonogenesis / stress-activated protein kinase signaling cascade / positive regulation of myoblast fusion / 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 / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / transforming growth factor beta receptor signaling pathway / cytokine activity / axon guidance / growth factor activity / positive regulation of neuron projection development / receptor tyrosine kinase binding / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / actin cytoskeleton / retina development in camera-type eye / cell-cell signaling / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / 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 / receptor complex / early endosome / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / axon / external side of plasma membrane / protein phosphorylation / focal adhesion / dendrite / neuronal cell body / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Li J / Shang GJ / Chen YJ / Brautigam CA / Liou J / Zhang XW / Bai XC | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20572.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-20572-v30.xml emd-20572.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_20572.png | 249.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20572 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20572 | HTTPS FTP |
-Related structure data
Related structure data | 6q2jMC 6q2nC 6q2oC 6q2rC 6q2sC 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_20572.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : RET, GFRAL and GDF15 extracellular complex
Entire | Name: RET, GFRAL and GDF15 extracellular complex |
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Components |
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-Supramolecule #1: RET, GFRAL and GDF15 extracellular complex
Supramolecule | Name: RET, GFRAL and GDF15 extracellular complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 200 kDa/nm |
-Macromolecule #1: Growth/differentiation factor 15
Macromolecule | Name: Growth/differentiation factor 15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.879113 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLEVLFQG PHMARNGDHC PLGPGRCCRL HTVRASLEDL GWADWVLSPR EVQVTMCIGA CPSQFRAANM HAQIKTSLH RLKPDTVPAP CCVPASYNPM VLIQKTDTGV SLQTYDDLLA KDCHCI |
-Macromolecule #2: GDNF family receptor alpha-like
Macromolecule | Name: GDNF family receptor alpha-like / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.120598 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QTNNCTYLRE QCLRDANGCK HAWRVMEDAC NDSDPGDPCK MRNSSYCNLS IQYLVESNFQ FKECLCTDDF YCTVNKLLGK KCINKSDNV KEDKFKWNLT TRSHHGFKGM WSCLEVAEAC VGDVVCNAQL ASYLKACSAN GNPCDLKQCQ AAIRFFYQNI P FNIAQMLA ...String: QTNNCTYLRE QCLRDANGCK HAWRVMEDAC NDSDPGDPCK MRNSSYCNLS IQYLVESNFQ FKECLCTDDF YCTVNKLLGK KCINKSDNV KEDKFKWNLT TRSHHGFKGM WSCLEVAEAC VGDVVCNAQL ASYLKACSAN GNPCDLKQCQ AAIRFFYQNI P FNIAQMLA FCDCAQSDIP CQQSKEALHS KTCAVNMVPP PTCLSVIRSC QNDELCRRHY RTFQSKCWQR VTRKCHEDEN CI STLSKQD LTCSGSDDCK AAYIDILGTV LQVQCTCRTI TQSEESLCKI FQHMLHRKSC FNYPTLSNVK GMALYTRKHA NKI TLTGFH SPFNGEVGTH HHHHHHH |
-Macromolecule #3: Proto-oncogene tyrosine-protein kinase receptor Ret
Macromolecule | Name: Proto-oncogene tyrosine-protein kinase receptor Ret / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 69.100812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LYFSRDAYWE KLYVDQAAGT PLLYVHALRD APEEVPSFRL GQHLYGTYRT RLHENNWICI QEDTGLLYLN RSLDHSSWEK LSVRNHGFP LLTVYLKVFL SPTSLREGEC QWPGCARVYF SFFNTSFPAC SSLKPRELCF PETRPSFRIR ENRPPGTFHQ F RLLPVQFL ...String: LYFSRDAYWE KLYVDQAAGT PLLYVHALRD APEEVPSFRL GQHLYGTYRT RLHENNWICI QEDTGLLYLN RSLDHSSWEK LSVRNHGFP LLTVYLKVFL SPTSLREGEC QWPGCARVYF SFFNTSFPAC SSLKPRELCF PETRPSFRIR ENRPPGTFHQ F RLLPVQFL CPNISVAYRL LEGEGLPFRC APDSLEVSTR WALDREQREK YELVAVCTVH AGAREEVVMV PFPVTVYDED DS APTFPAG VDTASAVVEF KRKEDTVVAT LRVFDADVVP ASGELVRRYT STLLPGDTWA QQTFRVEHWP NETSVQANGS FVR ATVHDY RLVLNRNLSI SENRTMQLAV LVNDSDFQGP GAGVLLLHFN VSVLPVSLHL PSTYSLSVSR RARRFAQIGK VCVE NCQAF SGINVQYKLH SSGANCSTLG VVTSAEDTSG ILFVNDTKAL RRPKCAELHY MVVATDQQTS RQAQAQLLVT VEGSY VAEE AGCPLSCAVS KRRLECEECG GLGSPTGRCE WRQGDGKGIT RNFSTCSPST KTCPDGHCDV VETQDINICP QDCLRG SIV GGHEPGEPRG IKAGYGTCNC FPEEEKCFCE PEDIQDPLCD ELCRGTHHHH HHHH |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 14 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 46729 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Average exposure time: 15.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: RELION |
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Startup model | Type of model: OTHER / Details: The initial model was generated in RELION. |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 520480 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 190 |
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Output model | PDB-6q2j: |