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- EMDB-12285: Platelet integrin from intact cells -

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Basic information

Entry
Database: EMDB / ID: EMD-12285
TitlePlatelet integrin from intact cells
Map dataPlatelet integrin from intact cells
Sample
  • Complex: Platelet integrin from intact cells
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 26.6 Å
AuthorsSorrentino 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
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179418 Switzerland
European Research Council (ERC)ERC-Syg HighResCellsEuropean Union
CitationJournal: 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
DepositionFeb 1, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12285.png

Downloads & links

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Map

FileDownload / File: emd_12285.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlatelet integrin from intact cells
Voxel sizeX=Y=Z: 4.4 Å
Density
Contour LevelBy AUTHOR: 0.0235 / Movie #1: 0.0235
Minimum - Maximum-0.40232125 - 0.37153998
Average (Standard dev.)0.0010106402 (±0.0317899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44.4
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-0.4020.3720.001

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Supplemental data

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Sample components

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Entire : Platelet integrin from intact cells

EntireName: Platelet integrin from intact cells
Components
  • Complex: Platelet integrin from intact cells

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Supramolecule #1: Platelet integrin from intact cells

SupramoleculeName: Platelet integrin from intact cells / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Tissue: platelet / Location in cell: cytoplasmic membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 5.1
GridModel: Quantifoil / Material: GOLD
VitrificationCryogen name: ETHANE
Detailscomplete human platelets

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.73 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 25 / Number images used: 40324 / Reference model: reference free / Method: pySeg software
Details: Automatic particle picking for membrane proteins based on disperse algorithm https://github.com/anmartinezs/pyseg_system
CTF correctionSoftware - Name: NOVACTF
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 26.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number subtomograms used: 7141
FSC plot (resolution estimation)

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