8JA5

Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8

Li, Y.H.Huang, X.Y.Li, R.H.Xu, J.J.Chen, W.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14F8 antibody heavy chainA [auth H],
D [auth B]
233Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
14F8 antibody light chainB [auth L]216Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein GC [auth A],
F [auth D]
423Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IH62 (Nipah virus)
Explore Q9IH62 
Go to UniProtKB:  Q9IH62
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UniProt GroupQ9IH62
Glycosylation
Glycosylation Sites: 4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
14F8 antibody light chainE [auth C]219Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-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-glucopyranoseH [auth F]6N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G],
J [auth I],
L [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-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-glucopyranoseK [auth J]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00395TQ
GlyCosmos:  G00395TQ
GlyGen:  G00395TQ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.957α = 90
b = 125.957β = 90
c = 317.264γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200762

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary