6N1W | pdb_00006n1w

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.1 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: https://doi.org/10.1016/j.cell.2019.06.030
  • Primary Citation 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
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 534.63 kDa 
  • Atom Count: 31,905 
  • Modeled Residue Count: 3,852 
  • Deposited Residue Count: 4,587 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A [auth 2],
I [auth C],
Q [auth c]
473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DFPH-a.15 heavy chainB [auth 3],
K [auth H],
S [auth h]
224Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DFPH-a.15 Light chainC [auth 4],
L,
T [auth l]
212Macaca mulattaMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 Heavy chainD [auth 5],
M,
U [auth m]
132Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 Light chainE [auth 6],
N,
V [auth n]
105Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 Light chainF [auth 7],
P [auth R],
X [auth r]
102Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 Heavy chainG [auth 8],
O [auth Q],
W [auth q]
128Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41H [auth A],
J [auth D],
R [auth d]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus type 1)
Explore Q2N0S7 
Go to UniProtKB:  Q2N0S7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S7
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth F],
AB [auth t],
BA [auth G],
BB [auth u],
CA [auth I],
AA [auth F],
AB [auth t],
BA [auth G],
BB [auth u],
CA [auth I],
CB [auth v],
EA [auth K],
EB [auth x],
FA [auth O],
FB [auth y],
JA [auth U],
JB [auth 9],
LA [auth W],
NA [auth Y],
OA [auth Z],
PA [auth a],
RA [auth e],
SA [auth f],
WA [auth k],
Y [auth B],
YA [auth p]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD 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
HA [auth S],
HB [auth 0],
KA [auth V],
KB [auth AA],
MA [auth X],
HA [auth S],
HB [auth 0],
KA [auth V],
KB [auth AA],
MA [auth X],
UA [auth i],
XA [auth o],
Z [auth E],
ZA [auth s]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD 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],
DB [auth w],
QA [auth b]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth P],
GB [auth z],
TA [auth g]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD 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 T],
IB [auth 1],
VA [auth j]
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
LB [auth 2]
MB [auth 2]
NB [auth 2]
OB [auth C]
PB [auth C]
LB [auth 2],
MB [auth 2],
NB [auth 2],
OB [auth C],
PB [auth C],
QB [auth C],
RB [auth c],
SB [auth c],
TB [auth c]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary