6CDI

Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.

Xu, K.Acharya, P.Kong, R.Cheng, C.Chuang, G.Y.Liu, K.Louder, M.K.O'Dell, S.Rawi, R.Sastry, M.Shen, C.H.Zhang, B.Zhou, T.Asokan, M.Bailer, R.T.Chambers, M.Chen, X.Choi, C.W.Dandey, V.P.Doria-Rose, N.A.Druz, A.Eng, E.T.Farney, S.K.Foulds, K.E.Geng, H.Georgiev, I.S.Gorman, J.Hill, K.R.Jafari, A.J.Kwon, Y.D.Lai, Y.T.Lemmin, T.McKee, K.Ohr, T.Y.Ou, L.Peng, D.Rowshan, A.P.Sheng, Z.Todd, J.P.Tsybovsky, Y.Viox, E.G.Wang, Y.Wei, H.Yang, Y.Zhou, A.F.Chen, R.Yang, L.Scorpio, D.G.McDermott, A.B.Shapiro, L.Carragher, B.Potter, C.S.Mascola, J.R.Kwong, P.D.

(2018) Nat Med 24: 857-867

  • DOI: 10.1038/s41591-018-0042-6
  • Primary Citation of Related Structures:  
    5TKK, 5TKJ, 6CDP, 6CDO, 6CDI, 6CDM, 6CDE

  • PubMed Abstract: 
  • A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses ...

    A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. pdkwong@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoprotein gp41I [auth A], Q [auth D], A [auth c]153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
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Go to UniProtKB:  Q2N0S7
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoprotein 120J [auth 2], R [auth C], B [auth d]473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 Light ChainK [auth 6], S [auth N], C [auth n]107Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 Heavy ChainL [auth 5], T [auth M], D [auth m]132Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 light chainM [auth 7], U [auth R], E [auth r]102Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 Heavy ChainN [auth 8], V [auth Q], F [auth q]227Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
vFP16.02 Heavy ChainO [auth 3], W [auth H], G [auth h]211Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
vFP16.02 Light ChainP [auth 4], X [auth L], H [auth l]216Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth t], FA [auth O], GB [auth z], JA [auth U], NB [auth DA], PA [auth a], RB [auth HA], WA [auth k]
AB [auth t], FA [auth O], GB [auth z], JA [auth U], NB [auth DA], PA [auth a], RB [auth HA], WA [auth k], Y [auth B]
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 10
MoleculeChainsChain 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-glucopyranose
BA [auth G], FB [auth y], HB [auth 0], JB [auth 9], OA [auth Z], QA [auth b], SA [auth f], WB [auth MA]
BA [auth G], FB [auth y], HB [auth 0], JB [auth 9], OA [auth Z], QA [auth b], SA [auth f], WB [auth MA], Z [auth E]
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth F], CB [auth v], EB [auth x], HA [auth S], IA [auth T], IB [auth 1], LA [auth W], NA [auth Y]
AA [auth F], CB [auth v], EB [auth x], HA [auth S], IA [auth T], IB [auth 1], LA [auth W], NA [auth Y], PB [auth FA], QB [auth GA], RA [auth e], TB [auth JA], VB [auth LA], YA [auth p], ZA [auth s]
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 12
MoleculeChainsChain 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)-2-acetamido-2-deoxy-beta-D-glucopyranoseBB [auth u], CA [auth I], KA [auth V], KB [auth AA], SB [auth IA], TA [auth g]5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 13
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth J], LB [auth BA], UA [auth i]8 N-Glycosylation Oligosaccharides Interaction
Entity ID: 14
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth K], MB [auth CA], VA [auth j]4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 15
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth P], OB [auth EA], XA [auth o]6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 16
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDB [auth w], MA [auth X], UB [auth KA]9 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 General Medical Sciences (NIH/NIGMS)United StatesGM103310
National Institutes of Health/Office of the DirectorUnited StatesS10 OD019994-01
Simons FoundationUnited States349247

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 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, Other, Structure summary