+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12285 | |||||||||
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Title | Platelet integrin from intact cells | |||||||||
Map data | Platelet integrin from intact cells | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 26.6 Å | |||||||||
Authors | Sorrentino S / Conesa JJ / Cuervo A / Melero R / Martins B / Fernandez-Gimenez E / Isidro-Gomez F / Jimenez de la Morena J / Studt JD / Sorzano COS ...Sorrentino S / Conesa JJ / Cuervo A / Melero R / Martins B / Fernandez-Gimenez E / Isidro-Gomez F / Jimenez de la Morena J / Studt JD / Sorzano COS / Eibauer M / Carazo JM / Medalia O | |||||||||
Funding support | Switzerland, European Union, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structural analysis of receptors and actin polarity in platelet protrusions. Authors: Simona Sorrentino / Jose Javier Conesa / Ana Cuervo / Roberto Melero / Bruno Martins / Estrella Fernandez-Gimenez / Federico P de Isidro-Gomez / Jimenez de la Morena / Jan-Dirk Studt / ...Authors: Simona Sorrentino / Jose Javier Conesa / Ana Cuervo / Roberto Melero / Bruno Martins / Estrella Fernandez-Gimenez / Federico P de Isidro-Gomez / Jimenez de la Morena / Jan-Dirk Studt / Carlos Oscar S Sorzano / Matthias Eibauer / Jose Maria Carazo / Ohad Medalia / Abstract: During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. ...During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. Initially, this task relies on the formation of strong cellular-extracellular matrix interactions, exposed in subendothelial lesions. Despite the medical relevance of these processes, there is a lack of high-resolution structural information on the platelet cytoskeleton controlling cell spreading and adhesion. Here, we present in situ structural analysis of membrane receptors and the underlying cytoskeleton in platelet protrusions by applying cryoelectron tomography to intact platelets. We utilized three-dimensional averaging procedures to study receptors at the plasma membrane. Analysis of substrate interaction-free receptors yielded one main structural class resolved to 26 Å, resembling the αβ integrin folded conformation. Furthermore, structural analysis of the actin network in pseudopodia indicates a nonuniform polarity of filaments. This organization would allow generation of the contractile forces required for integrin-mediated cell adhesion. | |||||||||
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_12285.map.gz | 227.3 KB | EMDB map data format | |
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Header (meta data) | emd-12285-v30.xml emd-12285.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12285_fsc.xml | 1.2 KB | Display | FSC data file |
Images | emd_12285.png | 41.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12285 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12285 | HTTPS FTP |
-Validation report
Summary document | emd_12285_validation.pdf.gz | 332.3 KB | Display | EMDB validaton report |
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Full document | emd_12285_full_validation.pdf.gz | 331.9 KB | Display | |
Data in XML | emd_12285_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_12285_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12285 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12285 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10636 (Title: Structural analysis of receptors and actin polarity in platelet protrusions Data size: 6.0 Data #1: Structural analysis of receptors and actin polarity in platelet protrusions [reconstructed volumes]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12285.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Platelet integrin from intact cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.4 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 : Platelet integrin from intact cells
Entire | Name: Platelet integrin from intact cells |
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Components |
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-Supramolecule #1: Platelet integrin from intact cells
Supramolecule | Name: Platelet integrin from intact cells / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: platelet / Location in cell: cytoplasmic membrane |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 5.1 |
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Grid | Model: Quantifoil / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
Details | complete human platelets |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.73 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |