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- EMDB-20572: Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 -

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Basic information

Entry
Database: EMDB / ID: EMD-20572
TitleCryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15
Map dataCryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement.
Sample
  • Complex: RET, GFRAL and GDF15 extracellular complex
    • Protein or peptide: Growth/differentiation factor 15
    • Protein or peptide: GDNF family receptor alpha-like
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase receptor Ret
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsRET / receptor tyrosine kinase / cryo-EM / SIGNALING PROTEIN
Function / homology
Function and homology information


response to metformin / negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / GDF15-GFRAL signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway ...response to metformin / negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / GDF15-GFRAL signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / posterior midgut development / positive regulation of peptidyl-serine phosphorylation of STAT protein / membrane protein proteolysis / Formation of the ureteric bud / positive regulation of neuron maturation / neuron cell-cell adhesion / negative regulation of leukocyte migration / Formation of the nephric duct / positive regulation of fatty acid oxidation / enteric nervous system development / negative regulation of appetite / innervation / cellular response to chemical stress / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / stress-activated protein kinase signaling cascade / positive regulation of cell adhesion mediated by integrin / ureteric bud development / neural crest cell migration / negative regulation of multicellular organism growth / positive regulation of myoblast fusion / regulation of axonogenesis / response to pain / negative regulation of SMAD protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / RET signaling / positive regulation of cell size / 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 / axon guidance / cytokine activity / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / receptor protein-tyrosine kinase / hormone activity / : / receptor tyrosine kinase binding / positive regulation of neuron projection development / MAPK cascade / actin cytoskeleton / cell-cell signaling / retina development in camera-type eye / 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 / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / protein phosphorylation / axon / external side of plasma membrane / focal adhesion / neuronal cell body / dendrite / 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
Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 ...Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 / RET Cadherin like domain 3 / RET Cadherin like domain 4 / RET, Cysteine Rich Domain / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Cystine-knot cytokine / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase receptor Ret / GDNF family receptor alpha-like / Growth/differentiation factor 15
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi J / Shang GJ
CitationJournal: 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
DepositionAug 8, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q2j
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20572.png

Downloads & links

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Map

FileDownload / File: emd_20572.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.13880223 - 0.2098538
Average (Standard dev.)0.00041176175 (±0.0062563308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z256.800256.800256.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1390.2100.000

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Supplemental data

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Sample components

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Entire : RET, GFRAL and GDF15 extracellular complex

EntireName: RET, GFRAL and GDF15 extracellular complex
Components
  • Complex: RET, GFRAL and GDF15 extracellular complex
    • Protein or peptide: Growth/differentiation factor 15
    • Protein or peptide: GDNF family receptor alpha-like
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase receptor Ret
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: RET, GFRAL and GDF15 extracellular complex

SupramoleculeName: RET, GFRAL and GDF15 extracellular complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: Growth/differentiation factor 15

MacromoleculeName: Growth/differentiation factor 15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.879113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLEVLFQG PHMARNGDHC PLGPGRCCRL HTVRASLEDL GWADWVLSPR EVQVTMCIGA CPSQFRAANM HAQIKTSLH RLKPDTVPAP CCVPASYNPM VLIQKTDTGV SLQTYDDLLA KDCHCI

UniProtKB: Growth/differentiation factor 15

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Macromolecule #2: GDNF family receptor alpha-like

MacromoleculeName: GDNF family receptor alpha-like / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.120598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: GDNF family receptor alpha-like

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Macromolecule #3: Proto-oncogene tyrosine-protein kinase receptor Ret

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.100812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Proto-oncogene tyrosine-protein kinase receptor Ret

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 14 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 46729 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen 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

Startup modelType of model: OTHER / Details: The initial model was generated in RELION.
Final reconstructionApplied 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
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 190
Output model

PDB-6q2j:
Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15

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