+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27411 | |||||||||
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Title | Ectodomain of full-length KIT(T417I,delta418-419)-SCF dimers | |||||||||
Map data | Ectodomain local refinement of KIT(T417I,delta418-419)-SCF dimers | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants ...positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / stem cell factor receptor activity / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / erythropoietin-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / positive regulation of dendritic cell cytokine production / Kit signaling pathway / positive regulation of melanocyte differentiation / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / mast cell apoptotic process / mast cell differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / myeloid leukocyte differentiation / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / positive regulation of mast cell cytokine production / immature B cell differentiation / melanocyte differentiation / germ cell migration / lymphoid progenitor cell differentiation / myeloid progenitor cell differentiation / digestive tract development / positive regulation of Ras protein signal transduction / negative regulation of programmed cell death / neural crest cell migration / embryonic hemopoiesis / lamellipodium assembly / pigmentation / positive regulation of leukocyte migration / tongue development / megakaryocyte development / Regulation of KIT signaling / mast cell degranulation / stem cell population maintenance / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / spermatid development / growth factor binding / somatic stem cell population maintenance / hemopoiesis / T cell differentiation / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / response to cadmium ion / positive regulation of phospholipase C activity / T cell proliferation / ovarian follicle development / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SH2 domain binding / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / B cell differentiation / erythrocyte differentiation / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / filopodium / epithelial cell proliferation / cytokine activity / stem cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / visual learning / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / response to organic cyclic compound / receptor protein-tyrosine kinase / fibrillar center / cytokine-mediated signaling pathway / male gonad development Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
Authors | Krimmer SG / Bertoletti N / 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_27411.map.gz | 212.7 MB | EMDB map data format | |
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Header (meta data) | emd-27411-v30.xml emd-27411.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27411_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_27411.png | 59.7 KB | ||
Masks | emd_27411_msk_1.map | 421.9 MB | Mask map | |
Others | emd_27411_additional_1.map.gz emd_27411_half_map_1.map.gz emd_27411_half_map_2.map.gz | 398.4 MB 391.5 MB 391.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27411 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27411 | HTTPS FTP |
-Related structure data
Related structure data | 8dfqMC 8dfmC 8dfpC M: atomic model generated by this map 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27411.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Ectodomain local refinement of KIT(T417I,delta418-419)-SCF dimers | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.4167 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27411_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Sharpened main map
File | emd_27411_additional_1.map | ||||||||||||
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Annotation | Sharpened main map | ||||||||||||
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Density Histograms |
-Half map: Half map A of main map
File | emd_27411_half_map_1.map | ||||||||||||
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Annotation | Half map A of main map | ||||||||||||
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Density Histograms |
-Half map: Half map B of main map
File | emd_27411_half_map_2.map | ||||||||||||
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Annotation | Half map B of main map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Full-length KIT(T417I,delta418-419)-SCF dimers reconstituted in a...
Entire | Name: Full-length KIT(T417I,delta418-419)-SCF dimers reconstituted in amphipol |
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Components |
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-Supramolecule #1: Full-length KIT(T417I,delta418-419)-SCF dimers reconstituted in a...
Supramolecule | Name: Full-length KIT(T417I,delta418-419)-SCF dimers reconstituted in amphipol type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Isoform 2 of Mast/stem cell growth factor receptor Kit
Macromolecule | Name: Isoform 2 of Mast/stem cell growth factor receptor Kit type: protein_or_peptide / ID: 1 / 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: 110.390805 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTILCWLALL STLTAVNADY KDDDDKRPHA MGEPSPPSIH PGKSDLIVRV GDEIRLLCTD PGFVKWTFEI LDETNENKQN EWITEKAEA TNTGKYTCTN KHGLSNSIYV FVRDPAKLFL VDRSLYGKED NDTLVRCPLT DPEVTNYSLK GCQGKPLPKD L RFIPDPKA ...String: MTILCWLALL STLTAVNADY KDDDDKRPHA MGEPSPPSIH PGKSDLIVRV GDEIRLLCTD PGFVKWTFEI LDETNENKQN EWITEKAEA TNTGKYTCTN KHGLSNSIYV FVRDPAKLFL VDRSLYGKED NDTLVRCPLT DPEVTNYSLK GCQGKPLPKD L RFIPDPKA GIMIKSVKRA YHRLCLHCSV DQEGKSVLSE KFILKVRPAF KAVPVVSVSK ASYLLREGEE FTVTCTIKDV SS SVYSTWK RENSQTKLQE KYNSWHHGDF NYERQATLTI SSARVNDSGV FMCYANNTFG SANVTTTLEV VDKGFINIFP MIN TTVFVN DGENVDLIVE YEAFPKPEHQ QWIYMNRTFT DKWEDYPKSE NESNIRYVSE LHLTRLKGTE GGTYTFLVSN SDVN AAIAF NVYVNTKPEI LIRLVNGMLQ CVAAGFPEPT IDWYFCPGTE QRCSASVLPV DVQTLNSSGP PFGKLVVQSS IDSSA FKHN GTVECKAYND VGKTSAYFNF AFKEQIHPHT LFTPLLIGFV IVAGMMCIIV MILTYKYLQK PMYEVQWKVV EEINGN NYV YIDPTQLPYD HKWEFPRNRL SFGKTLGAGA FGKVVEATAY GLIKSDAAMT VAVAMLKPSA HLTEREALMS ELKVLSY LG NHMNIVNLLG ACTIGGPTLV ITEYCCYGDL LNFLRRKRDS FICSKQEDHA EAALYKNLLH SKESSCSDST NEYMDMKP G VSYVVPTKAD KRRSVRIGSY IERDVTPAIM EDDELALDLE DLLSFSYQVA KGMAFLASKN CIHRDLAARN ILLTHGRIT KICDFGLARD IKNDSNYVVK GNARLPVKWM APESIFNCVY TFESDVWSYG IFLWELFSLG SSPYPGMPVD SKFYKMIKEG FRMLSPEHA PAEMYDIMKT CWDADPLKRP TFKQIVQLIE KQISESTNHI YSNLANCSPN RQKPVVDHSV RINSVGSTAS S SQPLLVHD DVGSHHHHHH |
-Macromolecule #2: Soluble KIT ligand
Macromolecule | Name: Soluble KIT ligand / 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: 16.007306 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: EGICRNRVTN NVKDVTKLVA NLPKDYMITL KYVPGMDVLP SHCWISEMVV QLSDSLTDLL DKFSNISEGL SNYSIIDKLV NIVDDLVEC VKENSSKDLK KSFKSPEPRL FTPEEFFRIF NRSIDAFKDF VVASETSDCV VS |
-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: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
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: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16476 / Average exposure time: 1.52 sec. / Average electron dose: 49.31 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |