8K0C | pdb_00008k0c

Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer.

Fan, P.Sun, M.Zhang, X.Zhang, H.Liu, Y.Yao, Y.Li, M.Fang, T.Sun, B.Chen, Z.Chi, X.Chen, L.Peng, C.Chen, Z.Zhang, G.Ren, Y.Liu, Z.Li, Y.Li, J.Li, E.Guan, W.Li, S.Gong, R.Zhang, K.Yu, C.Chiu, S.

(2024) Nat Commun 15: 4330-4330

  • DOI: https://doi.org/10.1038/s41467-024-48601-w
  • Primary Citation Related Structures: 
    8K0C, 8K0D, 8XC4

  • PubMed Abstract: 

    The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) glycoproteins required for virus entry remains unclear. Here, we isolate a panel of Macaca-derived G-specific antibodies that cross-neutralize HNVs via multiple mechanisms. The most potent antibody, 1E5, confers adequate protection against the Nipah virus challenge in female hamsters. Crystallography demonstrates that 1E5 has a highly similar binding pattern to the receptor. In cryo-electron microscopy studies, the tendency of 1E5 to bind to the upper or lower heads results in two distinct quaternary structures of G. Furthermore, we identify the extended outer loop β1S2-β1S3 of G and two pockets on the apical region of fusion (F) glycoprotein as the essential sites for G-F interactions. This work highlights promising drug candidates against HNVs and contributes deeper insights into the viruses.


  • Organizational Affiliation
    • Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China. fanpengfei93@163.com.

Macromolecule Content 

  • Total Structure Weight: 223.1 kDa 
  • Atom Count: 15,262 
  • Modeled Residue Count: 1,986 
  • Deposited Residue Count: 2,036 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of 1E5 Fab fragmentsA [auth E],
E [auth G]
242Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of 1E5 Fab fragmentsB [auth F],
F [auth H]
213Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GC [auth A],
G [auth B]
505Henipavirus nipahenseMutation(s): 0 
Gene Names: G
UniProt
Find proteins for Q9IH62 (Nipah virus)
Explore Q9IH62 
Go to UniProtKB:  Q9IH62
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IH62
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GD [auth C],
H [auth D]
58Henipavirus nipahenseMutation(s): 0 
Gene Names: G
UniProt
Find proteins for Q9IH62 (Nipah virus)
Explore Q9IH62 
Go to UniProtKB:  Q9IH62
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IH62
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-05-01 
  • Deposition Author(s): Sun, M.M.

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB0490000

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-23
    Changes: Data collection