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 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
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: S, 2
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: 11Go to GlyGen: P0DTC2-1
Sequence Annotations
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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