7KI4

Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing antibody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins.

Dang, H.V.Cross, R.W.Borisevich, V.Bornholdt, Z.A.West, B.R.Chan, Y.P.Mire, C.E.Da Silva, S.C.Dimitrov, A.S.Yan, L.Amaya, M.Navaratnarajah, C.K.Zeitlin, L.Geisbert, T.W.Broder, C.C.Veesler, D.

(2021) Nat Struct Mol Biol 28: 426-434

  • DOI: https://doi.org/10.1038/s41594-021-00584-8
  • Primary Citation of Related Structures:  
    7KI4, 7KI6

  • PubMed Abstract: 

    Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50-100%. There are no licensed therapeutics or vaccines to protect humans. HeV and NiV use a receptor-binding glycoprotein (G) and a fusion glycoprotein (F) to enter host cells. HNV F and G are the main targets of the humoral immune response, and the presence of neutralizing antibodies is a correlate of protection against NiV and HeV in experimentally infected animals. We describe here two cross-reactive F-specific antibodies, 1F5 and 12B2, that neutralize NiV and HeV through inhibition of membrane fusion. Cryo-electron microscopy structures reveal that 1F5 and 12B2 recognize distinct prefusion-specific, conserved quaternary epitopes and lock F in its prefusion conformation. We provide proof-of-concept for using antibody cocktails for neutralizing NiV and HeV and define a roadmap for developing effective countermeasures against these highly pathogenic viruses.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0A,
D [auth B],
G [auth E]
543Henipavirus 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
12B2 Fab light chainB [auth L],
E [auth C],
H [auth F]
214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
12B2 heavy chainC [auth H],
F [auth D],
I [auth G]
443Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth I],
L [auth K],
N,
P,
R,
J [auth I],
L [auth K],
N,
P,
R,
T
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
O,
S
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[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-glucopyranose
M, Q, U
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesDP1AI158186
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references