7TY0 | pdb_00007ty0

Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (local refinement of the stalk region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7TY0

This is version 1.3 of the entry. See complete history

Literature

Architecture and antigenicity of the Nipah virus attachment glycoprotein.

Wang, Z.Amaya, M.Addetia, A.Dang, H.V.Reggiano, G.Yan, L.Hickey, A.C.DiMaio, F.Broder, C.C.Veesler, D.

(2022) Science 375: 1373-1378

  • DOI: https://doi.org/10.1126/science.abm5561
  • Primary Citation Related Structures: 
    7TXZ, 7TY0

  • PubMed Abstract: 

    Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment (G) and fusion (F) glycoproteins, which are the main targets of antibody responses. To understand viral infection and host immunity, we determined a cryo-electron microscopy structure of the NiV G homotetrameric ectodomain in complex with the nAH1.3 broadly neutralizing antibody Fab fragment. We show that a cocktail of two nonoverlapping G-specific antibodies neutralizes NiV and HeV synergistically and limits the emergence of escape mutants. Analysis of polyclonal serum antibody responses elicited by vaccination of macaques with NiV G indicates that the receptor binding head domain is immunodominant. These results pave the way for implementing multipronged therapeutic strategies against these deadly pathogens.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 395.65 kDa 
  • Atom Count: 10,640 
  • Modeled Residue Count: 1,522 
  • Deposited Residue Count: 3,508 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GA,
B,
G [auth D],
H [auth C]
539Henipavirus nipahenseMutation(s): 0 
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
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Igh proteinC [auth J],
D [auth K]
458Mus sp.Mutation(s): 0 
Gene Names: Igh
UniProt
Find proteins for I6L985 (Mus musculus)
Explore I6L985 
Go to UniProtKB:  I6L985
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6L985
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
nAH Fab light chainE [auth N],
F [auth O]
218Mus sp.Mutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I [auth E],
J [auth F],
K [auth G],
L [auth H],
O [auth M],
I [auth E],
J [auth F],
K [auth G],
L [auth H],
O [auth M],
P
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth I]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth L]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2022-04-06
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary