8Z2E | pdb_00008z2e

Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Super broad and protective nanobodies against Sarbecoviruses including SARS-CoV-1 and the divergent SARS-CoV-2 subvariant KP.3.1.1.

Dong, H.Zhou, R.Chen, J.Wei, J.Wei, Z.Yang, Z.Zhu, K.Yang, Y.Yang, Q.Liu, N.Chen, Y.Wu, Y.Liang, Y.Zeng, Y.Guo, Q.Li, M.Shan, S.Wang, H.Niu, M.Yunfei Zeng, I.Shi, X.Zhang, Q.Wang, X.Chen, Z.Zhang, L.

(2024) PLoS Pathog 20: e1012625-e1012625

  • DOI: https://doi.org/10.1371/journal.ppat.1012625
  • Primary Citation Related Structures: 
    8Z2E

  • PubMed Abstract: 

    The ongoing evolution and immune escape of SARS-CoV-2, alongside the potential threat of SARS-CoV-1 and other sarbecoviruses, underscore the urgent need for effective strategies against their infection and transmission. This study highlights the discovery of nanobodies from immunized alpacas, which demonstrate exceptionally broad and potent neutralizing capabilities against the recently emerged and more divergent SARS-CoV-2 Omicron subvariants including JD.1.1, JN.1, KP.3, KP.3.1.1, as well as SARS-CoV-1 and coronaviruses from bats and pangolins utilizing receptor ACE2. Among these, Tnb04-1 emerges as the most broad and potent, binding to a conserved hydrophobic pocket in the spike's receptor-binding domain, distinct from the ACE2 binding site. This interaction disrupts the formation of a proteinase K-resistant core, crucial for viral-cell fusion. Notably, intranasal administration of Tnb04-1 in Syrian hamsters effectively prevented respiratory infection and transmission of the authentic Omicron XBB.1.5 subvariant. Thus, Thb04-1 holds promise in combating respiratory acquisition and transmission of diverse sarbecoviruses.


  • Organizational Affiliation
    • Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 83.81 kDa 
  • Atom Count: 5,963 
  • Modeled Residue Count: 737 
  • Deposited Residue Count: 764 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tnb04-1A [auth B]116Vicugna pacosMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1B [auth E]217Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
1F11-HC [auth H]217Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
1F11-LD [auth L]214Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.142α = 90
b = 89.747β = 90
c = 127.345γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references