|Entry||Database: EMDB / ID: EMD-12285|
|Title||Platelet integrin from intact cells|
|Sample||Platelet integrin from intact cells|
|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 |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_12285.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 4.4 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Platelet integrin from intact cells
|Entire||Name: Platelet integrin from intact cells / Number of Components: 1|
-Component #1: protein, Platelet integrin from intact cells
|Protein||Name: Platelet integrin from intact cells / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (natural)||Location in cell: cytoplasmic membrane / Organ Or Tissue: platelet|
|Specimen||Specimen State: Cell / Method: cryo EM|
|Sample solution||pH: 5.1|
|Vitrification||Cryogen Name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.73 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Imaging Mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi