8XC4

Nipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5

• PDB DOI: https://doi.org/10.2210/pdb8XC4/pdb

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


• Deposited: 2023-12-08 Released: 2024-01-24 
• Deposition Author(s): Fan, P.F., Yu, C.M., Chen, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Nipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5

Fan, P.F., Yu, C.M., Chen, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 202.35 kDa 
• Atom Count: 13,778 
• Modelled Residue Count: 1,736 
• Deposited Residue Count: 1,790 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A, B	439	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q4VCP5 (Nipah virus) Explore Q4VCP5  Go to UniProtKB:  Q4VCP5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1E5-VH	C, E	242	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1E5-VL	D, F	214	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, K	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF GlyCosmos:  G42466VF GlyGen:  G42466VF

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G92953ND GlyCosmos:  G92953ND

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	M [auth A], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.422	α = 90
b = 193.422	β = 90
c = 198.111	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Fan, P.F., Yu, C.M., Chen, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82204260

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release