9DZ2 | pdb_00009dz2

Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with hNPC1-C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with its human endosomal receptor NPC1.

Bu, F.Ye, G.Turner-Hubbard, H.Herbst, M.Liu, B.Li, F.

(2025) Commun Biol 8: 156-156

  • DOI: https://doi.org/10.1038/s42003-025-07613-y
  • Primary Citation of Related Structures:  
    9DZ2

  • PubMed Abstract: 

    Sudan ebolavirus (SUDV), like Ebola ebolavirus (EBOV), poses a significant threat to global health and security due to its high lethality. However, unlike EBOV, there are no approved vaccines or treatments for SUDV, and its structural interaction with the endosomal receptor NPC1 remains unclear. This study compares the glycoproteins of SUDV and EBOV (in their proteolytically primed forms) and their binding to human NPC1 (hNPC1). The findings reveal that the SUDV glycoprotein binds significantly more strongly to hNPC1 than the EBOV glycoprotein. Using cryo-EM, we determined the structure of the SUDV glycoprotein/hNPC1 complex, identifying four key residues in the SUDV glycoprotein that differ from those in the EBOV glycoprotein and influence hNPC1 binding: Ile79, Ala141, and Pro148 enhance binding, while Gln142 reduces it. Collectively, these residue differences account for SUDV's stronger binding affinity for hNPC1. This study provides critical insights into receptor recognition across all viruses in the ebolavirus genus, including their interactions with receptors in bats, their suspected reservoir hosts. These findings advance our understanding of ebolavirus cell entry, tissue tropism, and host range.


  • Organizational Affiliation
    • Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NPC intracellular cholesterol transporter 1A [auth C],
F [auth D]
280Homo sapiensMutation(s): 0 
Gene Names: NPC1
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens)
Explore O15118 
Go to UniProtKB:  O15118
PHAROS:  O15118
GTEx:  ENSG00000141458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15118
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinB [auth I],
D [auth A],
G [auth E]
195Sudan ebolavirusMutation(s): 0 
Gene Names: GP
UniProt
Find proteins for Q7T9D9 (Sudan ebolavirus (strain Human/Uganda/Gulu/2000))
Explore Q7T9D9 
Go to UniProtKB:  Q7T9D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T9D9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Shed GPC [auth J],
E [auth B],
H [auth F]
165Sudan ebolavirusMutation(s): 0 
Gene Names: GP
UniProt
Find proteins for Q7T9D9 (Sudan ebolavirus (strain Human/Uganda/Gulu/2000))
Explore Q7T9D9 
Go to UniProtKB:  Q7T9D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T9D9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI171954

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references