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- EMDB-23568: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralis... -

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Basic information

Entry
Database: EMDB / ID: EMD-23568
TitleCryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
Map data
SampleCryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry):
neutralising nanobodies WNb2 and WNb10 / (SARS-CoV-2 Spike ...) x 2 / WNb2 / Wnb10
Function / homology
Function and homology information


Translation of structural proteins / Virion Assembly and Release / Maturation of spike protein / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding ...Translation of structural proteins / Virion Assembly and Release / Maturation of spike protein / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / viral protein processing / 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 / 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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : ...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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPymm P / Tham W-H / Glukhova A
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
Wellcome Trust208693/Z/17/Z Australia
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice.
Authors: Phillip Pymm / Amy Adair / Li-Jin Chan / James P Cooney / Francesca L Mordant / Cody C Allison / Ester Lopez / Ebene R Haycroft / Matthew T O'Neill / Li Lynn Tan / Melanie H Dietrich / ...Authors: Phillip Pymm / Amy Adair / Li-Jin Chan / James P Cooney / Francesca L Mordant / Cody C Allison / Ester Lopez / Ebene R Haycroft / Matthew T O'Neill / Li Lynn Tan / Melanie H Dietrich / Damien Drew / Marcel Doerflinger / Michael A Dengler / Nichollas E Scott / Adam K Wheatley / Nicholas A Gherardin / Hariprasad Venugopal / Deborah Cromer / Miles P Davenport / Raelene Pickering / Dale I Godfrey / Damian F J Purcell / Stephen J Kent / Amy W Chung / Kanta Subbarao / Marc Pellegrini / Alisa Glukhova / Wai-Hong Tham /
Abstract: Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas ...Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensin-converting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 10-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.
History
DepositionMar 3, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23568.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 416 pix.
= 357.76 Å
0.86 Å/pix.
x 416 pix.
= 357.76 Å
0.86 Å/pix.
x 416 pix.
= 357.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.017
Minimum - Maximum-0.045408927 - 0.09531523
Average (Standard dev.)8.319037e-05 (±0.0033905872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 357.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z357.760357.760357.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0450.0950.000

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Supplemental data

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Additional map: refine3D map

Fileemd_23568_additional_1.map
Annotationrefine3D map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralis...

EntireName: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
Number of components: 6

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Component #1: protein, Cryo-EM map of SARS-CoV-2 Spike protein in complex with ...

ProteinName: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
Recombinant expression: No

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Component #2: protein, neutralising nanobodies WNb2 and WNb10

ProteinName: neutralising nanobodies WNb2 and WNb10 / Recombinant expression: No
SourceSpecies: Vicugna pacos (alpaca)

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Component #3: protein, SARS-CoV-2 Spike protein

ProteinName: SARS-CoV-2 Spike protein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #4: protein, SARS-CoV-2 Spike protein

ProteinName: SARS-CoV-2 Spike protein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #5: protein, WNb2

ProteinName: WNb2 / Recombinant expression: No
SourceSpecies: Vicugna pacos (alpaca)

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Component #6: protein, Wnb10

ProteinName: Wnb10 / Recombinant expression: No
SourceSpecies: Vicugna pacos (alpaca)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 55.9 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 22923
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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