7NS6 | pdb_00007ns6

SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7NS6

This is version 1.1 of the entry. See complete history

Literature

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo.

Hanke, L.Das, H.Sheward, D.J.Perez Vidakovics, L.Urgard, E.Moliner-Morro, A.Kim, C.Karl, V.Pankow, A.Smith, N.L.Porebski, B.Fernandez-Capetillo, O.Sezgin, E.Pedersen, G.K.Coquet, J.M.Hallberg, B.M.Murrell, B.McInerney, G.M.

(2022) Nat Commun 13: 155-155

  • DOI: https://doi.org/10.1038/s41467-021-27610-z
  • Primary Citation Related Structures: 
    7NLL, 7NS6

  • PubMed Abstract: 

    Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.


  • Organizational Affiliation
    • Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 961.37 kDa 
  • Atom Count: 55,899 
  • Modeled Residue Count: 7,109 
  • Deposited Residue Count: 8,598 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fu2 nanobody145Vicugna pacosMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein,Fibritin1,288Severe acute respiratory syndrome coronavirus 2Tequatrovirus T4
This entity is chimeric
Mutation(s): 0 
Gene Names: S2wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2P10104
Glycosylation
Glycosylation Sites: 8Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth A],
N [auth B]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth K]
AB [auth N]
BA [auth K]
BB [auth N]
CA [auth K]
AA [auth K],
AB [auth N],
BA [auth K],
BB [auth N],
CA [auth K],
CB [auth N],
DA [auth M],
DB [auth N],
EA [auth M],
EB [auth N],
FA [auth M],
FB [auth N],
GA [auth M],
GB [auth N],
HA [auth M],
HB [auth N],
IA [auth M],
JA [auth M],
KA [auth M],
LA [auth M],
MA [auth M],
NA [auth J],
O [auth I],
OA [auth J],
P [auth I],
PA [auth J],
Q [auth I],
QA [auth J],
R [auth I],
RA [auth J],
S [auth I],
SA [auth J],
T [auth I],
TA [auth J],
U [auth I],
UA [auth J],
V [auth I],
VA [auth L],
W [auth K],
WA [auth L],
X [auth K],
XA [auth L],
Y [auth K],
YA [auth L],
Z [auth K],
ZA [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.1.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary