8XKI | pdb_00008xki

A neutralizing nanobody VHH60 against wt SARS-CoV-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8XKI

This is version 1.2 of the entry. See complete history

Literature

A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug.

Liu, Q.Lu, Y.Cai, C.Huang, Y.Zhou, L.Guan, Y.Fu, S.Lin, Y.Yan, H.Zhang, Z.Li, X.Yang, X.Yang, H.Guo, H.Lan, K.Chen, Y.Hou, S.C.Xiong, Y.

(2024) Cell Death Dis 15: 458-458

  • DOI: https://doi.org/10.1038/s41419-024-06802-7
  • Primary Citation Related Structures: 
    8XK2, 8XKI

  • PubMed Abstract: 

    SARS-CoV-2 infection is initiated by Spike glycoprotein binding to the human angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain. Blocking this interaction has been proven to be an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody named VHH60, which was directly produced from an engineering nanobody library based on a commercialized nanobody within a very short period. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein at S 351 , S 470-471 and S 493-494 as determined by structural analysis, with an affinity of 2.56 nM. It inhibits infections of both ancestral SARS-CoV-2 strain and pseudotyped viruses harboring SARS-CoV-2 wildtype, key mutations or variants at the nanomolar level. Furthermore, VHH60 suppressed SARS-CoV-2 infection and propagation 50-fold better and protected mice from death for twice as long as the control group after SARS-CoV-2 nasal infections in vivo. Therefore, VHH60 is not only a powerful nanobody with a promising profile for disease control but also provides evidence for a highly effective and rapid approach to generating therapeutic nanobodies.


  • Organizational Affiliation
    • State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.

Macromolecule Content 

  • Total Structure Weight: 447.42 kDa 
  • Atom Count: 24,431 
  • Modeled Residue Count: 3,121 
  • Deposited Residue Count: 3,985 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
nanobody VHH60A [auth D]121synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinB [auth A],
C [auth B],
D [auth C]
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 9 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 8Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E [auth K],
F [auth O],
G [auth P],
H [auth Q],
I [auth T],
E [auth K],
F [auth O],
G [auth P],
H [auth Q],
I [auth T],
J [auth W]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
K [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government92169109
Other governmentZD2021CY001

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection