6NF2

Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.

Kong, R.Duan, H.Sheng, Z.Xu, K.Acharya, P.Chen, X.Cheng, C.Dingens, A.S.Gorman, J.Sastry, M.Shen, C.H.Zhang, B.Zhou, T.Chuang, G.Y.Chao, C.W.Gu, Y.Jafari, A.J.Louder, M.K.O'Dell, S.Rowshan, A.P.Viox, E.G.Wang, Y.Choi, C.W.Corcoran, M.M.Corrigan, A.R.Dandey, V.P.Eng, E.T.Geng, H.Foulds, K.E.Guo, Y.Kwon, Y.D.Lin, B.Liu, K.Mason, R.D.Nason, M.C.Ohr, T.Y.Ou, L.Rawi, R.Sarfo, E.K.Schon, A.Todd, J.P.Wang, S.Wei, H.Wu, W.Mullikin, J.C.Bailer, R.T.Doria-Rose, N.A.Karlsson Hedestam, G.B.Scorpio, D.G.Overbaugh, J.Bloom, J.D.Carragher, B.Potter, C.S.Shapiro, L.Kwong, P.D.Mascola, J.R.

(2019) Cell 178: 567-584.e19

  • DOI: 10.1016/j.cell.2019.06.030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked fiv ...

    The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.


    Organizational Affiliation

    Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.,Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.,Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.,Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: jmascola@nih.gov.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA.,National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Electronic address: pdkwong@nih.gov.,Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120
A, G, Q
480Human immunodeficiency virus 1Mutation(s): 7 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp41
B, I, R
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VRC03 Heavy Chain
C, N, V
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VRC03 Light Chain
D, M, U
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT122 Heavy Chain
E, J, S
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT122 Light Chain
F, K, T
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
0PV-c.01 Heavy Chain
H, O, W
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
0PV-c.01 Light Chain
L, P, X
219N/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, G, Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection, Database references