9UAA | pdb_00009uaa

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent Cross-neutralizing Antibodies Reveal Vulnerabilities of Henipavirus Fusion Glycoprotein.

Ren, Y.Fan, P.Zhang, X.Fang, T.Chen, Z.Yao, Y.Chi, X.Zhang, G.Zhao, X.Sun, B.Li, F.Liu, Z.Song, Z.Zhang, B.Peng, C.Li, E.Yang, Y.Li, J.Chiu, S.Yu, C.

(2025) Adv Sci (Weinh) 12: e2501996-e2501996

  • DOI: https://doi.org/10.1002/advs.202501996
  • Primary Citation of Related Structures:  
    9UA9, 9UAA

  • PubMed Abstract: 

    Hendra and Nipah viruses (HNVs), zoonotic paramyxoviruses with >50% case fatality rates, cause fatal encephalitis and respiratory disease, yet lack approved therapies. Here, nine rhesus-derived monoclonal antibodies (mAbs) targeting the fusion glycoprotein (F) prefusion conformation are developed. Four mAbs exhibit first-rate cross-neutralization against HNVs, with two showing synergistic potency when combined with attachment glycoprotein (G)-specific mAbs. Single-dose administration of mAbs confers robust protection against lethal Nipah virus challenge in hamsters. Structural insights reveal that 8 of the 9 potent mAbs adopt a human IGHV4-59-like framework with protruding CDRH3 loops, forming pushpin-shaped paratopes that stabilize the prefusion F-trimer by occupying vulnerable interprotomer cavities. Systematic mutational profiling identifies 14 prefusion-locking residues within the F ectodomain, classified as i) structural linchpins governing fusogenicity or ii) immunodominant hotspots targeted by cross-neutralizing mAbs. This work delivers promising therapeutic candidates against HNVs and provides blueprints for the rational design of antibodies and vaccines targeting viral fusion machinery.


  • Organizational Affiliation
    • School of Medicine, Zhejiang University, Hangzhou, 310058, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0A,
F [auth B],
G [auth C]
445Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IH63 (Nipah virus)
Explore Q9IH63 
Go to UniProtKB:  Q9IH63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IH63
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5C8-VLB [auth F],
H [auth E],
I [auth D]
106MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
5C8-VHC [auth G],
D [auth H],
E [auth I]
127MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth B]
N [auth B]
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 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
Other governmentChinaJCKY2020802B001

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references