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- EMDB-11728: SARS-CoV-2 spike glycoprotein bound to nanobodies (Ty1) -

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Basic information

Entry
Database: EMDB / ID: EMD-11728
TitleSARS-CoV-2 spike glycoprotein bound to nanobodies (Ty1)
Map data
SampleSARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1):
SARS-CoV-2 spike glycoprotein / Nanobody Ty1
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHallberg BM / Das H
Citation
Journal: Nat Commun / Year: 2020
Title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.
Authors: Leo Hanke / Laura Vidakovics Perez / Daniel J Sheward / Hrishikesh Das / Tim Schulte / Ainhoa Moliner-Morro / Martin Corcoran / Adnane Achour / Gunilla B Karlsson Hedestam / B Martin ...Authors: Leo Hanke / Laura Vidakovics Perez / Daniel J Sheward / Hrishikesh Das / Tim Schulte / Ainhoa Moliner-Morro / Martin Corcoran / Adnane Achour / Gunilla B Karlsson Hedestam / B Martin Hällberg / Ben Murrell / Gerald M McInerney /
Abstract: SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive ...SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.
#1: Journal: BiorXiv / Year: 2020
Title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction
Authors: Hanke L / Vidakovics Perez L / Sheward DJ / Das H / Schulte T / Moliner-Morro A / Corcoran M / Achour A / Karlsson Hedestam G / Hallberg BM / Murrell B / McInerney GM
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 15, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11728.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 428 pix.
= 436.56 Å
1.02 Å/pix.
x 428 pix.
= 436.56 Å
1.02 Å/pix.
x 428 pix.
= 436.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.27 / Movie #1: 0.2
Minimum - Maximum-0.8010464 - 1.6954437
Average (Standard dev.)-0.00032490134 (±0.030576892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions428428428
Spacing428428428
CellA=B=C: 436.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z428428428
origin x/y/z0.0000.0000.000
length x/y/z436.560436.560436.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ428428428
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS428428428
D min/max/mean-0.8011.695-0.000

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Supplemental data

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Segmentation: #1

Fileemd_11728_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: locally sharpened map

Fileemd_11728_half_map_1.map
Annotationlocally sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 1

Fileemd_11728_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)

EntireName: SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)
Number of components: 3

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Component #1: protein, SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)

ProteinName: SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)
Recombinant expression: No
MassTheoretical: 470 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, SARS-CoV-2 spike glycoprotein

ProteinName: SARS-CoV-2 spike glycoprotein / Details: SARS-CoV-2 spike glycoprotein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Nanobody Ty1

ProteinName: Nanobody Ty1 / Recombinant expression: No
SourceSpecies: Vicugna pacos (alpaca)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.7 mg/mL / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: A 3-ul aliquot of the sample solution was applied 335to glow-discharged CryoMatrix holey grids with amorphous alloy film (Zhenjiang Lehua Technology) in 336a Vitrobot Mk IV (Thermo Fisher ...Details: A 3-ul aliquot of the sample solution was applied 335to glow-discharged CryoMatrix holey grids with amorphous alloy film (Zhenjiang Lehua Technology) in 336a Vitrobot Mk IV (Thermo Fisher Scientific) at 4 degrees and 100% humidity (blot 10 s, blot force 3)..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 300.0 - 2500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 210832
3D reconstructionSoftware: cryoSPARC / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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