8F7T

Glycan-Base ConC Env Trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases.

Olia, A.S.Cheng, C.Zhou, T.Biju, A.Harris, D.R.Changela, A.Duan, H.Ivleva, V.B.Kong, W.P.Ou, L.Rawi, R.Tsybovsky, Y.Van Wazer, D.J.Corrigan, A.R.Gonelli, C.A.Lee, M.McKee, K.Narpala, S.O'Dell, S.Parchment, D.K.Stancofski, E.D.Stephens, T.Tan, I.Teng, I.T.Wang, S.Wei, Q.Yang, Y.Yang, Z.Zhang, B.Novak, J.Renfrow, M.B.Doria-Rose, N.A.Koup, R.A.McDermott, A.B.Gall, J.G.Lei, Q.P.Mascola, J.R.Kwong, P.D.

(2023) iScience 26: 107403-107403

  • DOI: https://doi.org/10.1016/j.isci.2023.107403
  • Primary Citation of Related Structures:  
    8F7T

  • PubMed Abstract: 

    Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential N -linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.


  • Organizational Affiliation

    Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env gp41
A, B, D
156Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env gp120C,
E,
F [auth G]
479Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth I],
H [auth K],
I [auth L]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G35932AR
GlyCosmos:  G35932AR
GlyGen:  G35932AR
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
L [auth C]
M [auth C]
N [auth C]
J [auth A],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth E],
R [auth E],
S [auth E],
T [auth E],
U [auth G],
V [auth G],
W [auth G],
X [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release