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- EMDB-26794: Tomogram of platelet filopodia in presence of SARS-CoV-2 spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-26794
TitleTomogram of platelet filopodia in presence of SARS-CoV-2 spike protein
Map dataTomogram of platelet filopodia in presence of SARS-CoV-2 spike protein
Sample
  • Cell: Platelet deformation induced by SARS-CoV-2 spike protein
    • Organelle or cellular component: platelet
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodelectron tomography / cryo EM
AuthorsKuhn CC / Basnet N / Bodakuntla S / Nichols S / Martinez-Sanchez A / Agostini L / Soh YM / Takagi J / Biertumpfel C / Mizuno N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein.
Authors: Christopher Cyrus Kuhn / Nirakar Basnet / Satish Bodakuntla / Pelayo Alvarez-Brecht / Scott Nichols / Antonio Martinez-Sanchez / Lorenzo Agostini / Young-Min Soh / Junichi Takagi / Christian ...Authors: Christopher Cyrus Kuhn / Nirakar Basnet / Satish Bodakuntla / Pelayo Alvarez-Brecht / Scott Nichols / Antonio Martinez-Sanchez / Lorenzo Agostini / Young-Min Soh / Junichi Takagi / Christian Biertümpfel / Naoko Mizuno /
Abstract: SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of ...SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of COVID-19 is the occurrence of coagulopathies. Here, we report the direct observation of the interactions between S protein and platelets. Live imaging shows that the S protein triggers platelets to deform dynamically, in some cases, leading to their irreversible activation. Cellular cryo-electron tomography reveals dense decorations of S protein on the platelet surface, inducing filopodia formation. Hypothesizing that S protein binds to filopodia-inducing integrin receptors, we tested the binding to RGD motif-recognizing platelet integrins and find that S protein recognizes integrin αβ. Our results infer that the stochastic activation of platelets is due to weak interactions of S protein with integrin, which can attribute to the pathogenesis of COVID-19 and the occurrence of rare but severe coagulopathies.
History
DepositionApr 27, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26794.png

Downloads & links

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Map

FileDownload / File: emd_26794.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of platelet filopodia in presence of SARS-CoV-2 spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.04 Å/pix.
x 464 pix.
= 5122.56 Å		11.04 Å/pix.
x 1440 pix.
= 15897.6 Å		11.04 Å/pix.
x 1023 pix.
= 11293.92 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.04 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-14.314463 - 10.575753
Average (Standard dev.)0.0010638427 (±0.22624522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-7676-84
Dimensions14401023464
Spacing10231440464
CellA: 11293.92 Å / B: 15897.6 Å / C: 5122.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Platelet deformation induced by SARS-CoV-2 spike protein

EntireName: Platelet deformation induced by SARS-CoV-2 spike protein
Components
  • Cell: Platelet deformation induced by SARS-CoV-2 spike protein
    • Organelle or cellular component: platelet
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Platelet deformation induced by SARS-CoV-2 spike protein

SupramoleculeName: Platelet deformation induced by SARS-CoV-2 spike protein
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: platelet

SupramoleculeName: platelet / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Details: isolated from whole blood

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Supramolecule #3: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: all

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: "SPIKE_SARS2 Spike glycoprotein(UniProt P0DTC2) RRAR furin cleavage site mutated to GSAGC-terminal Rho1D4-tag(TETSQVAPA) fused with spacer GSSG"
Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSAGSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDKVEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQYI KWPWYIWLGF IAGLIAIVMV TIMLCCMTSC CSCLKGCCSC GSCCKFDEDD SEPVLKGVKL HYTGSSGTET SQVAPA

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 61 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

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