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Yorodumi- EMDB-1977: Extracellular complexes of the hematopoietic human and mouse CSF-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1977 | |||||||||
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Title | Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles. | |||||||||
Map data | Surface rendering of the hCSF-1RD1-D5 hCSF-1 complex | |||||||||
Sample |
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Keywords | Hematopoiesis / Receptor Tyrosine Kinase (RTK) / Colony-Stimulating Factor-1 / CSF-1 / CSF-1R / ternary complex / ectodomain complex / cytokine-receptor complex | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Elegheert J / Desfosses A / Shkumatov AV / Wu X / Bracke N / Verstraete K / Van Craenenbroeck K / Brooks BR / Svergun DI / Vergauwen B ...Elegheert J / Desfosses A / Shkumatov AV / Wu X / Bracke N / Verstraete K / Van Craenenbroeck K / Brooks BR / Svergun DI / Vergauwen B / Gutsche I / Savvides SN | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles. Authors: Jonathan Elegheert / Ambroise Desfosses / Alexander V Shkumatov / Xiongwu Wu / Nathalie Bracke / Kenneth Verstraete / Kathleen Van Craenenbroeck / Bernard R Brooks / Dmitri I Svergun / Bjorn ...Authors: Jonathan Elegheert / Ambroise Desfosses / Alexander V Shkumatov / Xiongwu Wu / Nathalie Bracke / Kenneth Verstraete / Kathleen Van Craenenbroeck / Bernard R Brooks / Dmitri I Svergun / Bjorn Vergauwen / Irina Gutsche / Savvas N Savvides / Abstract: The hematopoietic colony stimulating factor-1 receptor (CSF-1R or FMS) is essential for the cellular repertoire of the mammalian immune system. Here, we report a structural and mechanistic consensus ...The hematopoietic colony stimulating factor-1 receptor (CSF-1R or FMS) is essential for the cellular repertoire of the mammalian immune system. Here, we report a structural and mechanistic consensus for the assembly of human and mouse CSF-1:CSF-1R complexes. The EM structure of the complete extracellular assembly of the human CSF-1:CSF-1R complex reveals how receptor dimerization by CSF-1 invokes a ternary complex featuring extensive homotypic receptor contacts and striking structural plasticity at the extremities of the complex. Studies by small-angle X-ray scattering of unliganded hCSF-1R point to large domain rearrangements upon CSF-1 binding, and provide structural evidence for the relevance of receptor predimerization at the cell surface. Comparative structural and binding studies aiming to dissect the assembly principles of human and mouse CSF-1R complexes, including a quantification of the CSF-1/CSF-1R species cross-reactivity, show that bivalent cytokine binding to receptor coupled to ensuing receptor-receptor interactions are common denominators in extracellular complex formation. | |||||||||
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_1977.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-1977-v30.xml emd-1977.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | 1977_CSF1R_imagedeposition.png | 30 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1977 | HTTPS FTP |
-Validation report
Summary document | emd_1977_validation.pdf.gz | 200.7 KB | Display | EMDB validaton report |
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Full document | emd_1977_full_validation.pdf.gz | 199.8 KB | Display | |
Data in XML | emd_1977_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1977 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1977 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1977.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface rendering of the hCSF-1RD1-D5 hCSF-1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.5 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 : Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the co...
Entire | Name: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R |
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Components |
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-Supramolecule #1000: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the co...
Supramolecule | Name: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Dimeric / Number unique components: 2 |
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Molecular weight | Experimental: 145 KDa / Theoretical: 145 KDa / Method: Multi-angle laser light scattering |
-Macromolecule #1: Colony Stimulating Factor-1 Receptor (CSF-1R)
Macromolecule | Name: Colony Stimulating Factor-1 Receptor (CSF-1R) / type: protein_or_peptide / ID: 1 / Name.synonym: CSF-1R / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 76 KDa / Theoretical: 76 KDa |
Recombinant expression | Organism: Homo sapiens, HEK293T cell line / Recombinant plasmid: pHLSec |
-Macromolecule #2: Colony Stimulating Factor-1
Macromolecule | Name: Colony Stimulating Factor-1 / type: protein_or_peptide / ID: 2 / Name.synonym: CSF-1 / Number of copies: 2 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Homo sapiens, HEK293T cell line / Recombinant plasmid: pHLSec |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 20 mM NaPO4 pH 7.40, 150 mM NaCl. |
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Staining | Type: NEGATIVE Details: Purified sample at 0.2 mg/mL in PBS buffer was applied to the clear side of carbon on a carbon-mica interface and stained by floating on 2 % (w/v) uranyl acetate. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1200EXII |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.1 mm / Nominal magnification: 40000 |
Sample stage | Specimen holder: Jeol / Specimen holder model: JEOL |
-Image processing
CTF correction | Details: CTFFIND3. Each particle |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER / Number images used: 9421 |