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- EMDB-11347: Structure of SARS-CoV-2 spike glycoprotein (S) trimer with one re... -

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Basic information

Entry
Database: EMDB / ID: EMD-11347
TitleStructure of SARS-CoV-2 spike glycoprotein (S) trimer with one receptor binding domain (RBD) in open-state determined by subtomogram averaging
Map dataMasked and sharpened map of the S protein with 1 open RBD.
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / viral life cycle / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / viral life cycle / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S2 / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 5.4 Å
AuthorsTuronova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C ...Turonova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C / van Zandbergen G / Laundry J / de Azevedo NTD / Mosalaganti S / Schwarz A / Covino R / Muhlebach M / Hummer G / Locker JK / Beck M
CitationJournal: Science / Year: 2020
Title: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van ...Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van Zandbergen / Jonathan Landry / Nayara Trevisan Doimo de Azevedo / Shyamal Mosalaganti / Andre Schwarz / Roberto Covino / Michael D Mühlebach / Gerhard Hummer / Jacomine Krijnse Locker / Martin Beck /
Abstract: The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo- ...The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.
History
DepositionJul 9, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11347.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked and sharpened map of the S protein with 1 open RBD.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 128 pix.
= 340.224 Å
2.66 Å/pix.
x 128 pix.
= 340.224 Å
2.66 Å/pix.
x 128 pix.
= 340.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.658 Å
Density
Contour LevelBy AUTHOR: 0.731 / Movie #1: 0.631
Minimum - Maximum-1.0319148 - 1.9635174
Average (Standard dev.)0.0147296265 (±0.1091061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 340.224 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.6582.6582.658
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z340.224340.224340.224
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.0321.9640.015

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Supplemental data

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Additional map: Raw map of the S protein with 1 open RBD.

Fileemd_11347_additional_1.map
AnnotationRaw map of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of the of the S protein with 1 open RBD.

Fileemd_11347_half_map_1.map
AnnotationHalf map of the of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of the of the S protein with 1 open RBD.

Fileemd_11347_half_map_2.map
AnnotationHalf map of the of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Formula: PBS / Component - Name: Phosphate buffered Saline
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 266 / Number images used: 78699 / Reference model: De Novo
CTF correctionSoftware:
Namedetails
CTFFIND
NOVACTFhttps://github.com/turonova/novaCTF
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 4217
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
RefinementProtocol: RIGID BODY FIT

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