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- EMDB-11144: SARS CoV-2 Spike protein, Closed conformation, C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-11144
TitleSARS CoV-2 Spike protein, Closed conformation, C1 symmetry
Map data
SampleSARS CoV-2 Spike protein, Closed conformation, C1 symmetry:
Spike glycoproteinPeplomer / (ligand) x 2
Function / homology
Function and homology information


suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsToelzer C / Gupta K / Yadav SKN / Burucu U / Schaffitzel C / Berger I
Funding support United Kingdom, 7 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P000940/1 United Kingdom
Wellcome Trust206181/Z/17/Z United Kingdom
Wellcome Trust202904/Z/16/Z United Kingdom
Wellcome Trust210701/Z/18/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000484/1 United Kingdom
Wellcome Trust106115/Z/14/Z United Kingdom
CitationJournal: Science / Year: 2020
Title: Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.
Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Ufuk Borucu / Andrew D Davidson / Maia Kavanagh Williamson / Deborah K Shoemark / Frederic Garzoni / Oskar Staufer / Rachel Milligan / ...Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Ufuk Borucu / Andrew D Davidson / Maia Kavanagh Williamson / Deborah K Shoemark / Frederic Garzoni / Oskar Staufer / Rachel Milligan / Julien Capin / Adrian J Mulholland / Joachim Spatz / Daniel Fitzgerald / Imre Berger / Christiane Schaffitzel /
Abstract: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the ...Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms that drive high infectivity, broad tissue tropism, and severe pathology. Our 2.85-angstrom cryo-electron microscopy structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains tightly bind the essential free fatty acid linoleic acid (LA) in three composite binding pockets. A similar pocket also appears to be present in the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). LA binding stabilizes a locked S conformation, resulting in reduced angiotensin-converting enzyme 2 (ACE2) interaction in vitro In human cells, LA supplementation synergizes with the COVID-19 drug remdesivir, suppressing SARS-CoV-2 replication. Our structure directly links LA and S, setting the stage for intervention strategies that target LA binding by SARS-CoV-2.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 6, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zb4
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11144.png

Downloads & links

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Map

FileDownload / File: emd_11144.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 231. Å		1.05 Å/pix.
x 220 pix.
= 231. Å		1.05 Å/pix.
x 220 pix.
= 231. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.03
Minimum - Maximum-0.17485434 - 0.25473827
Average (Standard dev.)0.00069369836 (±0.010043019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 230.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z231.000231.000231.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1750.2550.001

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Supplemental data

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Segmentation: #1

Fileemd_11144_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11144_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11144_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire SARS CoV-2 Spike protein, Closed conformation, C1 symmetry

EntireName: SARS CoV-2 Spike protein, Closed conformation, C1 symmetry
Number of components: 4

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Component #1: protein, SARS CoV-2 Spike protein, Closed conformation, C1 symmetry

ProteinName: SARS CoV-2 Spike protein, Closed conformation, C1 symmetry
Recombinant expression: No
MassTheoretical: 540 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 139.735922 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 25 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #4: ligand, LINOLEIC ACID

LigandName: LINOLEIC ACID / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.280445 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.2 mg/mL / pH: 7.5
VitrificationCryogen name: OTHER

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Electron microscopy imaging

ImagingMicroscope: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 60.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -0.8 - -2.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3289

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 136405
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 6VXX

6vxx

Output model

6zb4

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