6MPH

Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

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:  
    6MPG, 6MPH, 6MQC, 6MQE, 6MQM, 6MQR, 6MQS, 6N16, 6N1V, 6N1W, 6NF2, 6OSY, 6OT1

  • 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 five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time ...

    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: 

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: jmascola@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DF1W-a.01 heavy chainA [auth 1],
C [auth 3],
K [auth H]		118Macaca mulattaMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DF1W-a.01 Light chainB [auth 2],
D [auth 4],
L		112Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41E [auth 6],
I [auth D],
J [auth E]		153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
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UniProt GroupQ2N0S7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120F [auth A],
G [auth B],
H [auth C]		473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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UniProt GroupQ2N0S6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 heavy chainM,
Q [auth X],
R [auth Y]		132Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 Light ChainN,
S [auth Z],
T [auth a]		107Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 Heavy chainO [auth Q],
U [auth f],
V [auth g]		227Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 Light ChainP [auth R],
W [auth h],
X [auth i]		102Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D 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
BA [auth J],
BB [auth w],
JA [auth W],
JB [auth 9],
OA [auth j],
BA [auth J],
BB [auth w],
JA [auth W],
JB [auth 9],
OA [auth j],
WA [auth r],
Y [auth F],
YA [auth t]
5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth O],
DB [auth y],
GA [auth T],
GB [auth 5],
HA [auth U],
DA [auth O],
DB [auth y],
GA [auth T],
GB [auth 5],
HA [auth U],
HB [auth 7],
MA [auth d],
QA [auth l],
TA [auth o],
UA [auth p],
Z [auth G],
ZA [auth u]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D 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
AA [auth I],
AB [auth v],
LA [auth c],
LB [auth BA],
MB [auth CA],
AA [auth I],
AB [auth v],
LA [auth c],
LB [auth BA],
MB [auth CA],
NA [auth e],
NB [auth DA]
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 12
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth K],
CB [auth x],
EA [auth P],
EB [auth z],
IA [auth V],
CA [auth K],
CB [auth x],
EA [auth P],
EB [auth z],
IA [auth V],
IB [auth 8],
KA [auth b],
KB [auth AA],
PA [auth k],
RA [auth m],
VA [auth q],
XA [auth s]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 13
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseFA [auth S],
FB [auth 0],
SA [auth n]		6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary