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

  • 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. 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

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein gp41A [auth c],
I [auth A],
Q [auth D]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Explore Q2N0S7 
Go to UniProtKB:  Q2N0S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein 120B [auth d],
J [auth 2],
R [auth C]
473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Light ChainC [auth n],
K [auth 6],
S [auth N]
107Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Heavy ChainD [auth m],
L [auth 5],
T [auth M]
132Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VRC03 light chainE [auth r],
M [auth 7],
U [auth R]
102Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
VRC03 Heavy ChainF [auth q],
N [auth 8],
V [auth Q]
227Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
vFP16.02 Heavy ChainG [auth h],
O [auth 3],
W [auth H]
211Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
vFP16.02 Light ChainH [auth l],
P [auth 4],
X [auth L]
216Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 9
MoleculeChains 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],
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]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
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-glucopyranose
BA [auth G],
FB [auth y],
HB [auth 0],
JB [auth 9],
OA [auth Z],
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]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 12
MoleculeChains 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-glucopyranose
BB [auth u],
CA [auth I],
KA [auth V],
KB [auth AA],
SB [auth IA],
BB [auth u],
CA [auth I],
KA [auth V],
KB [auth AA],
SB [auth IA],
TA [auth g]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 13
MoleculeChains 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]
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Entity ID: 14
MoleculeChains 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]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 15
MoleculeChains 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]
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 16
MoleculeChains 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]
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 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