+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2648 | |||||||||
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Title | stem cell factor-induced intact KIT dimers | |||||||||
Map data | Reconstruction of intact, kinase-dead KIT-SCF complex | |||||||||
Sample |
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Keywords | KIT / c-Kit / SCF / stem cell factor / transmembrane / receptor tyrosine kinase / RTK | |||||||||
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 / melanocyte migration / positive regulation of melanocyte differentiation / mast cell apoptotic process / positive regulation of mast cell proliferation ...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 / melanocyte migration / positive regulation of melanocyte differentiation / mast cell apoptotic process / positive regulation of mast cell proliferation / myeloid leukocyte differentiation / mast cell proliferation / positive regulation of Ras protein signal transduction / neural crest cell migration / embryonic hemopoiesis / positive regulation of leukocyte migration / Regulation of KIT signaling / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / T cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / filopodium / cytokine activity / growth factor activity / Signaling by SCF-KIT / response to organic cyclic compound / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / PIP3 activates AKT signaling / lamellipodium / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Ras protein signal transduction / cytoskeleton / cell adhesion / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.8 Å | |||||||||
Authors | Opatowsky Y / Bleichert F / Unger VM / Schlessinger J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers. Authors: Yarden Opatowsky / Irit Lax / Francisco Tomé / Franziska Bleichert / Vinzenz M Unger / Joseph Schlessinger / Abstract: Using electron microscopy and fitting of crystal structures, we present the 3D reconstruction of ligand-induced dimers of intact receptor tyrosine kinase, KIT. We observe that KIT protomers form ...Using electron microscopy and fitting of crystal structures, we present the 3D reconstruction of ligand-induced dimers of intact receptor tyrosine kinase, KIT. We observe that KIT protomers form close contacts throughout the entire structure of ligand-bound receptor dimers, and that the dimeric receptors adopt multiple, defined conformational states. Interestingly, the homotypic interactions in the membrane proximal Ig-like domain of the extracellular region differ from those observed in the crystal structure of the unconstrained extracellular regions. We observe two prevalent conformations in which the tyrosine kinase domains interact asymmetrically. The asymmetric arrangement of the cytoplasmic regions may represent snapshots of molecular interactions occurring during trans autophosphorylation. Moreover, the asymmetric arrangements may facilitate specific intermolecular interactions necessary for trans phosphorylation of different KIT autophosphorylation sites that are required for stimulation of kinase activity and recruitment of signaling proteins by activated KIT. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2648.map.gz | 971.5 KB | EMDB map data format | |
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Header (meta data) | emd-2648-v30.xml emd-2648.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_2648.png | 501.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2648 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2648 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2648.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of intact, kinase-dead KIT-SCF complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Intact human KIT dimer in complex with stem cell factor (SCF)dimer
Entire | Name: Intact human KIT dimer in complex with stem cell factor (SCF)dimer |
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Components |
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-Supramolecule #1000: Intact human KIT dimer in complex with stem cell factor (SCF)dimer
Supramolecule | Name: Intact human KIT dimer in complex with stem cell factor (SCF)dimer type: sample / ID: 1000 / Oligomeric state: one dimer of SCF binds to KIT dimer / Number unique components: 2 |
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Molecular weight | Theoretical: 290 KDa / Method: SDS-PAGE |
-Macromolecule #1: stem cell growth factor
Macromolecule | Name: stem cell growth factor / type: protein_or_peptide / ID: 1 / Name.synonym: SCF / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane |
Molecular weight | Theoretical: 15 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET11 |
Sequence | UniProtKB: Kit ligand |
-Macromolecule #2: KIT
Macromolecule | Name: KIT / type: protein_or_peptide / ID: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET11 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.4 / Details: 200mM NaCl, 20mM HEPES,15% glycerol, 0.05% DDM |
Staining | Type: NEGATIVE Details: grids with adsorbed protein were floated on 3 drops of 1% uranyl formate for 30 seconds each |
Grid | Details: 400 mesh copper grid with continuous thin carbon support over holy carbon film |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000 |
Sample stage | Specimen holder model: OTHER / Tilt angle max: 55 |
Date | Nov 27, 2008 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 400 / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
-Image processing
Final two d classification | Number classes: 3 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.8 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 1900 |
Details | Particles of tilt pairs (at 0 and 55 degrees)were manually selected using WEB. Initial reference-free alignment and classification of the untilted views was performed using IMAGIC-5. A representative class average was used for reference-based alignment, followed by cycles of multireference alignment and classification. Three out of 8 classes were used in random conical tilt reconstruction using SPIDER. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The domains were separately fitted by manual docking using Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The domains were separately fitted by manual docking using Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |