6MPG

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.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: 3.20 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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A12V163-b.01 Light ChainA [auth B],
K [auth 4],
X [auth Y]
113Macaca mulattaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B [auth U],
P [auth A],
R [auth D]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S7
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UniProt GroupQ2N0S7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C [auth V],
I [auth 2],
Q [auth C]
473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
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UniProt GroupQ2N0S6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
A12V163-b.01 Heavy ChainD [auth W],
J [auth 3],
W [auth X]
117Macaca mulattaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Heavy chainE [auth m],
L [auth 5],
S [auth M]
132Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Light chainF [auth n],
M [auth 6],
T [auth N]
107Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
VRC03 heavy chainG [auth q],
O [auth 8],
U [auth Q]
227Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
VRC03 Light chainH [auth r],
N [auth 7],
V [auth R]
102Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth G],
AB [auth t],
BA [auth H],
CA [auth I],
CB [auth v],
AA [auth G],
AB [auth t],
BA [auth H],
CA [auth I],
CB [auth v],
DB [auth w],
EA [auth K],
EB [auth x],
FA [auth L],
GB [auth z],
HB [auth 0],
JA [auth T],
LB [auth BA],
MA [auth b],
OA [auth d],
PA [auth e],
QA [auth f],
SA [auth h],
TA [auth i],
XA [auth o],
Y [auth E]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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
BB [auth u],
HA [auth P],
JB [auth 9],
KA [auth Z],
MB [auth CA],
BB [auth u],
HA [auth P],
JB [auth 9],
KA [auth Z],
MB [auth CA],
NA [auth c],
VA [auth k],
YA [auth p],
Z [auth F]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 11
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-glucopyranoseDA [auth J],
FB [auth y],
RA [auth g]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 12
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
GA [auth O],
IB [auth 1],
LA [auth a],
NB [auth DA],
UA [auth j],
GA [auth O],
IB [auth 1],
LA [auth a],
NB [auth DA],
UA [auth j],
ZA [auth s]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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)]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-glucopyranoseIA [auth S],
KB [auth AA],
WA [auth l]
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
OB [auth U]
PB [auth V]
QB [auth V]
RB [auth V]
SB [auth 2]
OB [auth U],
PB [auth V],
QB [auth V],
RB [auth V],
SB [auth 2],
TB [auth 2],
UB [auth 2],
VB [auth A],
WB [auth C],
XB [auth C],
YB [auth C],
ZB [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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 1.2: 2020-07-01
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary