8Y3U | pdb_00008y3u

Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection.

Fan, P.Sun, B.Liu, Z.Fang, T.Ren, Y.Zhao, X.Song, Z.Yang, Y.Li, J.Yu, C.Chen, W.

(2024) Emerg Microbes Infect 13: 2432366-2432366

  • DOI: https://doi.org/10.1080/22221751.2024.2432366
  • Primary Citation of Related Structures:  
    8Y3U

  • PubMed Abstract: 

    Orthoebolavirus is a genus of hazardous pathogens that has caused over 30 outbreaks. However, currently approved therapies are limited in scope, as they are only effective against the Ebola virus and lack cross-protection against other orthoebolaviruses. Here, we demonstrate that a previously isolated human-derived antibody, 2G1, can recognize the glycoprotein (GP) of every orthoebolavirus species. The cryo-electron microscopy structure of 2G1 Fab in complex with the GPΔMucin trimer reveals that 2G1 binds a quaternary pocket formed by three subunits from two GP protomers. 2G1 recognizes highly conserved epitopes among filoviruses and achieves neutralization by blocking GP proteolysis. We designed an efficient mRNA module capable of producing test antibodies at expression levels exceeding 1500 ng/mL in vitro. The lipid nanoparticle (LNP)-encapsulated mRNA-2G1 exhibited potent neutralizing activities against the HIV-pseudotyped Ebola and Sudan viruses that were 19.8 and 12.5 times that of IgG format, respectively. In mice, the antibodies encoded by the mRNA-2G1-LNP peaked within 24 h, effectively blocking the invasion of pseudoviruses with no apparent liver toxicity. This study suggests that the 2G1 antibody and its mRNA formulation represent promising candidate interventions for orthoebolavirus disease, and it provides an efficient mRNA framework applicable to antibody-based therapies.


  • Organizational Affiliation
    • Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, People's Republic of China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2G1 VH
A, E, I
124Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2G1 VL
B, F, J
105Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Virion spike glycoprotein
C, G, K
97Ebola virusMutation(s): 0 
Gene Names: GP
UniProt
Find proteins for A0A1C4HDV6 (Ebola virus)
Explore A0A1C4HDV6 
Go to UniProtKB:  A0A1C4HDV6
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UniProt GroupA0A1C4HDV6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SGP
D, H, L
157Ebola virusMutation(s): 0 
Gene Names: GP
UniProt
Find proteins for A0A1C4HDL5 (Ebola virus)
Explore A0A1C4HDL5 
Go to UniProtKB:  A0A1C4HDL5
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UniProt GroupA0A1C4HDL5
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O
5N/A
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82204260

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-02-19
    Changes: Data collection, Database references