6UDA

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 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

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: 10.1371/journal.ppat.1008026

  • 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 attr ...

    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 Medicine, Duke University Medical Center, Durham, NC, United States of America.,The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States of America.,Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America.,Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America.,Los Alamos National Laboratory, Theoretical Biology & Biophysics, Los Alamos, NM, United States of America.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.,Department of Surgery, Duke University Medical Center, Durham, NC, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CH505.N279K.G458Y.SOSIP.664 gp120
A, E, I
487Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for M4M0W3 (Human immunodeficiency virus 1)
Go to UniProtKB:  M4M0W3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CH235 UCA heavy chain Fab
C, G, K
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CH505.N279K.G458Y.SOSIP.664 gp41
Z, F, J
160Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CH235 UCA light chain Fab
D, H, L
234N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, E, I
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, E, I
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, E, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 AI145687-01

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release