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- EMDB-20579: Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20579 | |||||||||
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Title | Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry. | |||||||||
![]() | Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry. | |||||||||
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Function / homology | ![]() glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / 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 / SUMO is conjugated to E1 (UBA2:SAE1) ...glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / 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 / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / SUMOylation of transcription factors / axon guidance receptor activity / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / positive regulation of neuron maturation / Formation of the nephric duct / enteric nervous system development / SUMOylation of DNA damage response and repair proteins / neuron cell-cell adhesion / SUMOylation of DNA replication proteins / septin ring / sympathetic nervous system development / innervation / induction of positive chemotaxis / peripheral nervous system development / SUMOylation of SUMOylation proteins / plasma membrane protein complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / NCAM1 interactions / SUMOylation of RNA binding proteins / positive regulation of cell adhesion mediated by integrin / SUMOylation of chromatin organization proteins / neural crest cell migration / ureteric bud development / response to pain / regulation of axonogenesis / extrinsic component of membrane / ubiquitin-like protein ligase binding / homophilic cell adhesion via plasma membrane adhesion molecules / protein sumoylation / positive regulation of cell size / RET signaling / neuroblast proliferation / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / condensed nuclear chromosome / axon guidance / growth factor activity / neuron migration / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / PML body / positive regulation of neuron projection development / protein tag activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / retina development in camera-type eye / nervous system development / signaling receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / 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 / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / extracellular space / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Li J / Shang GJ / Chen YJ / Brautigam CA / Liou J / Zhang XW / Bai XC | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 240.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 489.1 KB | Display | ![]() |
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Full document | ![]() | 488.7 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6q2sMC ![]() 6q2jC ![]() 6q2nC ![]() 6q2oC ![]() 6q2rC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 200 kDa/nm |
-Macromolecule #1: Ubiquitin-like protein SMT3,Artemin
Macromolecule | Name: Ubiquitin-like protein SMT3,Artemin / type: protein_or_peptide / ID: 1 Details: A SUMO protein was fused to the N-terminal of NRTN for the protein expression Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.793287 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLRFL YDGIRIQADQ TPEDLDMEDN DIIEAHREQI GGSAGGPGSR ARAAGARGCR LRSQLVPVRA LGLGHRSDEL V RFRFCSGS ...String: MGSSHHHHHH SSGLVPRGSH MASMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLRFL YDGIRIQADQ TPEDLDMEDN DIIEAHREQI GGSAGGPGSR ARAAGARGCR LRSQLVPVRA LGLGHRSDEL V RFRFCSGS CRRARSPHDL SLASLLGAGA LRPPPGSRPV SQPCCRPTRY EAVSFMDVNS TWRTVDRLSA TACGCLG |
-Macromolecule #2: GDNF family receptor alpha-3
Macromolecule | Name: GDNF family receptor alpha-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 38.370023 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DPLPTESRLM NSCLQARRKC QADPTCSAAY HHLDSCTSSI STPLPSEEPS VPADCLEAAQ QLRNSSLIGC MCHRRMKNQV ACLDIYWTV HRARSLGNYE LDVSPYEDTV TSKPWKMNLS KLNMLKPDSD LCLKFAMLCT LNDKCDRLRK AYGEACSGPH C QRHVCLRQ ...String: DPLPTESRLM NSCLQARRKC QADPTCSAAY HHLDSCTSSI STPLPSEEPS VPADCLEAAQ QLRNSSLIGC MCHRRMKNQV ACLDIYWTV HRARSLGNYE LDVSPYEDTV TSKPWKMNLS KLNMLKPDSD LCLKFAMLCT LNDKCDRLRK AYGEACSGPH C QRHVCLRQ LLTFFEKAAE PHAQGLLLCP CAPNDRGCGE RRRNTIAPNC ALPPVAPNCL ELRRLCFSDP LCRSRLVDFQ TH CHPMDIL GTCATEQSRC LRAYLGLIGT AMTPNFVSNV NTSVALSCTC RGSGNLQEEC EMLEGFFSHN PCLTEAIAAK MRF HSQLFS QDWPHPGTHH HHHHHH |
-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: ![]() |
Molecular weight | Theoretical: 69.100812 KDa |
Recombinant expression | Organism: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 46729 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 190 |
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Output model | ![]() PDB-6q2s: |