9J7Y | pdb_00009j7y

the complex structure of MPXV M1R and nanobody M1R-01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.270 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of neutralizing nanobodies protecting against poxvirus infection.

Yang, X.Guo, L.Duan, H.Fan, M.Xu, F.Chi, X.Pan, S.Liu, X.Zhang, X.Gao, P.Zhang, F.Wang, X.Guo, F.Ge, J.Ren, L.Yang, W.

(2025) Cell Discov 11: 31-31

  • DOI: https://doi.org/10.1038/s41421-025-00771-7
  • Primary Citation of Related Structures:  
    9J7Y

  • PubMed Abstract: 

    An outbreak of mpox has triggered concerns regarding the adequacy of intervention strategies. Passive immunity conferred by neutralizing antibodies exhibits potential in the prophylaxis and treatment of orthopoxvirus infections. Despite this, the investigations of effective antibody therapeutics have been hindered by the varied nature of orthopoxvirus envelope proteins and the intricate mechanisms underpinning viral invasion. Our study involves the production of six mpox virus (MPXV) envelope proteins, which are relatively conservative and considered to play a role in the neutralization process. We employed a synthetic nanobody (Nb) library to derive a broad array of specific Nbs against these viral proteins. We identified a cross-reactive Nb, termed M1R-01, which targets the M1R protein and effectively neutralizes both vaccinia virus (VACV) and MPXV. Notably, the M1R-01-based antibody strategy provided optimal protection against a lethal VACV challenge in mice. Additionally, we determined the crystal structure of the M1R-Nb complex, uncovering novel binding attributes of M1R-01 and detailed conformational epitope information. This work provides a promising candidate for the therapy and prophylaxis of orthopoxvirus infections.


  • Organizational Affiliation
    • Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Entry-fusion complex associated protein OPG095A [auth G]191Monkeypox virusMutation(s): 0 
Gene Names: OPG099MPXVgp080
UniProt
Find proteins for M1LBP0 (Monkeypox virus)
Explore M1LBP0 
Go to UniProtKB:  M1LBP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1LBP0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody M1R-01B [auth H]123synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.27α = 90
b = 61.27β = 90
c = 167.499γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references