8XNH

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

• PDB DOI: https://doi.org/10.2210/pdb8XNH/pdb
• EM Map EMD-38504: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Henipavirus nipahense, Macaca
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-12-30 Released: 2024-07-10 
• Deposition Author(s): Fan, P.F., Ren, Y., Yu, C.M., Chen, W.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6

Fan, P.F., Yu, C.M., Chen, W., Ren, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 251.55 kDa 
• Atom Count: 15,706 
• Modelled Residue Count: 2,031 
• Deposited Residue Count: 2,277 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, H [auth B], I [auth C]	498	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IH63 (Nipah virus) Explore Q9IH63  Go to UniProtKB:  Q9IH63
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5C8-VL	B [auth D], C [auth E], D [auth F]	131	Macaca	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5C8-VH	E [auth G], F [auth H], G [auth I]	130	Macaca	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [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: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Fan, P.F., Ren, Y., Yu, C.M., Chen, W.

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Funding Organization	Location	Grant Number
Other government	China	JCKY2020802B001

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release