+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27496 | |||||||||
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Title | Full-length KIT(T417I,delta418-419) dimers | |||||||||
Map data | Relion 3D refinement | |||||||||
Sample |
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Keywords | receptor tyrosine kinase / cell signaling / cancer / cryo-EM / KIT / stem cell factor / oncogenic mutant / extracellular domain / asymmetric interface / structural plasticity / TRANSFERASE | |||||||||
Function / homology | receptor protein-tyrosine kinase / Isoform 2 of Mast/stem cell growth factor receptor Kit Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.1 Å | |||||||||
Authors | Bertoletti N / Krimmer SG / Mi W / Schlessinger J | |||||||||
Funding support | 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention. Authors: Stefan G Krimmer / Nicole Bertoletti / Yoshihisa Suzuki / Luka Katic / Jyotidarsini Mohanty / Sheng Shu / Sangwon Lee / Irit Lax / Wei Mi / Joseph Schlessinger / Abstract: The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as ...The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia, gastrointestinal stromal tumor, and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo electron microscopy (cryo-EM) structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the overall symmetric arrangement of the extracellular domain of ligand-occupied KIT dimers contains asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an "Achilles heel" for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. Binding of SCF to this mutant fully restores the conformation of wild-type KIT dimers, including the formation of salt bridges responsible for D4 homotypic contacts and other hallmarks of SCF-induced KIT dimerization. These experiments reveal an unexpected structural plasticity of oncogenic KIT mutants and a therapeutic target in D5. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27496.map.gz | 191.9 MB | EMDB map data format | |
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Header (meta data) | emd-27496-v30.xml emd-27496.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27496_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_27496.png | 17 KB | ||
Filedesc metadata | emd-27496.cif.gz | 5.7 KB | ||
Others | emd_27496_half_map_1.map.gz emd_27496_half_map_2.map.gz | 193.9 MB 194.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27496 | HTTPS FTP |
-Related structure data
Related structure data | 8dfmC 8dfpC 8dfqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27496.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Relion 3D refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.346 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half1
File | emd_27496_half_map_1.map | ||||||||||||
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Annotation | Half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2
File | emd_27496_half_map_2.map | ||||||||||||
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Annotation | Half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full-length KIT(T417I,delta418-419) dimers reconstituted in amphipol
Entire | Name: Full-length KIT(T417I,delta418-419) dimers reconstituted in amphipol |
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Components |
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-Supramolecule #1: Full-length KIT(T417I,delta418-419) dimers reconstituted in amphipol
Supramolecule | Name: Full-length KIT(T417I,delta418-419) dimers reconstituted in amphipol type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Mast/stem cell growth factor receptor Kit
Macromolecule | Name: Mast/stem cell growth factor receptor Kit / type: protein_or_peptide / ID: 1 Details: MTILCWLALLSTLTAVNA signal peptide NADYKDDDDKRPHAM expression tag (NAG) post-translational glycosylation Mutation T417I Deletion mutation Y418,D419 Mutation K623A GSHHHHHH expression tag Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTILCWLALL STLTAVNADY KDDDDKRPHA MGEPSPPSIH PGKSDLIVRV GDEIRLLCTD PGFVKWTFEI LDETNENKQN EWITEKAEAT NTGKYTCTNK HGLSNSIYVF VRDPAKLFLV DRSLYGKEDN DTLVRCPLTD PEVTNYSLKG CQGKPLPKDL RFIPDPKAGI ...String: MTILCWLALL STLTAVNADY KDDDDKRPHA MGEPSPPSIH PGKSDLIVRV GDEIRLLCTD PGFVKWTFEI LDETNENKQN EWITEKAEAT NTGKYTCTNK HGLSNSIYVF VRDPAKLFLV DRSLYGKEDN DTLVRCPLTD PEVTNYSLKG CQGKPLPKDL RFIPDPKAGI MIKSVKRAYH RLCLHCSVDQ EGKSVLSEKF ILKVRPAFKA VPVVSVSKAS YLLREGEEFT VTCTIKDVSS SVYSTWKREN SQTKLQEKYN SWHHGDFNYE RQATLTISSA RVNDSGVFMC YANNTFGSAN VTTTLEVVDK GFINIFPMIN TTVFVNDGEN VDLIVEYEAF PKPEHQQWIY MNRTFTDKWE DYPKSENESN IRYVSELHLT RLKGTEGGTY TFLVSNSDVN AAIAFNVYVN TKPEILIRLV NGMLQCVAAG FPEPTIDWYF CPGTEQRCSA SVLPVDVQTL NSSGPPFGKL VVQSSIDSSA FKHNGTVECK AYNDVGKTSA YFNFAFKEQI HPHTLFTPLL IGFVIVAGMM CIIVMILTYK YLQKPMYEVQ WKVVEEINGN NYVYIDPTQL PYDHKWEFPR NRLSFGKTLG AGAFGKVVEA TAYGLIKSDA AMTVAVAMLK PSAHLTEREA LMSELKVLSY LGNHMNIVNL LGACTIGGPT LVITEYCCYG DLLNFLRRKR DSFICSKQED HAEAALYKNL LHSKESSCSD STNEYMDMKP GVSYVVPTKA DKRRSVRIGS YIERDVTPAI MEDDELALDL EDLLSFSYQV AKGMAFLASK NCIHRDLAAR NILLTHGRIT KICDFGLARD IKNDSNYVVK GNARLPVKWM APESIFNCVY TFESDVWSYG IFLWELFSLG SSPYPGMPVD SKFYKMIKEG FRMLSPEHAP AEMYDIMKTC WDADPLKRPT FKQIVQLIEK QISESTNHIY SNLANCSPNR QKPVVDHSVR INSVGSTASS SQPLLVHDDV GSHHHHHH UniProtKB: Isoform 2 of Mast/stem cell growth factor receptor Kit |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.6 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Blotting time 3 sec, blotting force 0.. | ||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Details | SerialEM COMA-FREE ALIGNMENT |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8397 / Average exposure time: 11.134 sec. / Average electron dose: 64.76 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |