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- EMDB-11526: Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutra... -

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Basic information

Entry
Database: EMDB / ID: EMD-11526
TitleCryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)
Map data
SampleTernary complex between Nanobody Ty1 and Spike.
  • Nanobody strongly neutralising and blocks ACE2 binding.
  • (Nanobody Ty1) x 2
  • Spike glycoproteinPeplomer
  • ligand
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 / 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 L / Sheward DJ / 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
DepositionJul 30, 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: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zxn
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11526.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
AxesX (Sec.)Y (Row.)Z (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: 2.74 / Movie #1: 3
Minimum - Maximum-43.933025 - 77.14982
Average (Standard dev.)0.00055904285 (±0.9428028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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/S321
start NC/NR/NS000
NC/NR/NS428428428
D min/max/mean-43.93377.1500.001

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Supplemental data

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Sample components

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Entire Ternary complex between Nanobody Ty1 and Spike.

EntireName: Ternary complex between Nanobody Ty1 and Spike. / Number of components: 6

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Component #1: protein, Ternary complex between Nanobody Ty1 and Spike.

ProteinName: Ternary complex between Nanobody Ty1 and Spike. / Recombinant expression: No
MassTheoretical: 14 kDa

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Component #2: protein, Nanobody strongly neutralising and blocks ACE2 binding.

ProteinName: Nanobody strongly neutralising and blocks ACE2 binding.
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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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer
Details: Severe acute respiratory syndrome coronavirus 2 spike glykoprotein
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 142.399375 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Nanobody Ty1

ProteinName: Nanobody Ty1
Details: Nanobody Ty1 that neutralises SARS-CoV-2 by blocking the receptor bindings site on the spike glykoprotein
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 14.306924 kDa
SourceSpecies: Vicugna pacos (alpaca)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 39 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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: 51 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 Bioquantum
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: 131816
3D reconstructionAlgorithm: BACK PROJECTION / Software: cryoSPARC / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 6VSB
Output model

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