6UDA

Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancester of CH235 lineage CD4bs broadly neutralizing antibodies.

LaBranche, C.C.Henderson, R.Hsu, A.Behrens, S.Chen, X.Zhou, T.Wiehe, K.Saunders, K.O.Alam, S.M.Bonsignori, M.Borgnia, M.J.Sattentau, Q.J.Eaton, A.Greene, K.Gao, H.Liao, H.X.Williams, W.B.Peacock, J.Tang, H.Perez, L.G.Edwards, R.J.Kepler, T.B.Korber, B.T.Kwong, P.D.Mascola, J.R.Acharya, P.Haynes, B.F.Montefiori, D.C.

(2019) PLoS Pathog 15: e1008026-e1008026

  • DOI: https://doi.org/10.1371/journal.ppat.1008026
  • Primary Citation of Related Structures:  
    6UDA

  • PubMed Abstract: 

    The CD4 binding site (CD4bs) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies (bnAbs) that are attractive to elicit with vaccines. The CH235 lineage (VH1-46) of CD4bs bnAbs is particularly attractive because the most mature members neutralize 90% of circulating strains, do not possess long HCDR3 regions, and do not contain insertions and deletions that may be difficult to induce. We used virus neutralization to measure the interaction of CH235 unmutated common ancestor (CH235 UCA) with functional Env trimers on infectious virions to guide immunogen design for this bnAb lineage. Two Env mutations were identified, one in loop D (N279K) and another in V5 (G458Y), that acted synergistically to render autologous CH505 transmitted/founder virus susceptible to neutralization by CH235 UCA. Man5-enriched N-glycans provided additional synergy for neutralization. CH235 UCA bound with nanomolar affinity to corresponding soluble native-like Env trimers as candidate immunogens. A cryo-EM structure of CH235 UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 revealed interactions of the antibody light chain complementarity determining region 3 (CDR L3) with the engineered Env loops D and V5. These results demonstrate that virus neutralization can directly inform vaccine design and suggest a germline targeting and reverse engineering strategy to initiate and mature the CH235 bnAb lineage.


  • Organizational Affiliation

    Department of Surgery, Duke University Medical Center, Durham, NC, United States of America.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CH505.N279K.G458Y.SOSIP.664 gp120
A, E, I
487Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
UniProt
Find proteins for M4M0W3 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  M4M0W3
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UniProt GroupM4M0W3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CH235 UCA heavy chain FabB [auth C],
G,
K
249Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CH505.N279K.G458Y.SOSIP.664 gp41C [auth Z],
F,
J
160Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
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UniProt GroupQ2N0S5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CH235 UCA light chain Fab
D, H, L
234Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

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-glucopyranoseM [auth B],
N [auth M],
O [auth N]
4N/A
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI145687-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary