+Open data
-Basic information
Entry | Database: PDB / ID: 8dfq | ||||||
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Title | Ectodomain of full-length KIT(T417I,delta418-419)-SCF dimers | ||||||
Components |
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Keywords | TRANSFERASE / receptor tyrosine kinase / cell signaling / cancer / cryo-EM / KIT / stem cell factor / oncogenic mutant / extracellular domain / asymmetric interface / structural plasticity | ||||||
Function / homology | Function and homology information positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / 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 / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / 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 / myeloid leukocyte differentiation / 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 differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / tongue development / mast cell apoptotic process / 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 / immature B cell differentiation / melanocyte differentiation / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / germ cell migration / myeloid progenitor cell differentiation / digestive tract development / positive regulation of Ras protein signal transduction / negative regulation of programmed cell death / neural crest cell migration / positive regulation of leukocyte migration / embryonic hemopoiesis / lamellipodium assembly / megakaryocyte development / Regulation of KIT signaling / stem cell population maintenance / pigmentation / mast cell degranulation / positive regulation of Notch signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / growth factor binding / cytokine binding / somatic stem cell population maintenance / hemopoiesis / spermatid development / T cell differentiation / Transcriptional and post-translational regulation of MITF-M expression and activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ectopic germ cell programmed cell death / transmembrane receptor protein tyrosine kinase activity / hematopoietic progenitor cell differentiation / : / response to cadmium ion / T cell proliferation / positive regulation of T cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of tyrosine phosphorylation of STAT protein / epithelial cell proliferation / SH2 domain binding / B cell differentiation / cell chemotaxis / acrosomal vesicle / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / filopodium / cytokine activity / stem cell differentiation / receptor protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of DNA-binding transcription factor activity / growth factor activity / visual learning / Signaling by SCF-KIT / response to organic cyclic compound / cytoplasmic side of plasma membrane / Constitutive Signaling by Aberrant PI3K in Cancer Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||
Authors | Krimmer, S.G. / Bertoletti, N. / Mi, W. / Schlessinger, J. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dfq.cif.gz | 337 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dfq.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 8dfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dfq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8dfq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8dfq_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 8dfq_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/8dfq ftp://data.pdbj.org/pub/pdb/validation_reports/df/8dfq | HTTPS FTP |
-Related structure data
Related structure data | 27411MC 8dfmC 8dfpC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 110390.805 Da / Num. of mol.: 2 / Mutation: T417I, K619A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIT, SCFR / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P10721, receptor protein-tyrosine kinase #2: Protein | Mass: 16007.306 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KITLG, MGF, SCF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus RIPL / References: UniProt: P21583 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Full-length KIT(T417I,delta418-419)-SCF dimers reconstituted in amphipol Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.25 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Blotting time 3 sec, blotting force 0. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.52 sec. / Electron dose: 49.31 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16476 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2650475 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337995 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 145 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8DFM | ||||||||||||||||||||||||||||||||||||||||
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