6OSY | pdb_00006osy

Cryo-EM structure of vaccine-elicited antibody 0PV-a.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6OSY

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: 685.49 kDa 
  • Atom Count: 32,463 
  • Modeled Residue Count: 3,834 
  • Deposited Residue Count: 5,913 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 gp120A [auth 2],
G [auth B],
P [auth K]
480Human 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: 17
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 HeavyB [auth 5],
H [auth C],
R [auth M]
235Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 LightC [auth 6],
I [auth D],
S [auth N]
213Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 LightD [auth 7],
J [auth E],
T [auth O]
209Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 HeavyE [auth 8],
K [auth F],
U [auth P]
233Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 gp41F [auth A],
L [auth G],
V [auth Q]
153Human immunodeficiency virus 1Mutation(s): 0 
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: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
0PV-a.01 HeavyM [auth H],
N [auth I],
W [auth R]
235Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
0PV-a.01 LightO [auth J],
Q [auth L],
X [auth S]
213Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 9
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
AA [auth V],
DB [auth y],
EB [auth z],
GB [auth 1],
NA [auth i],
AA [auth V],
DB [auth y],
EB [auth z],
GB [auth 1],
NA [auth i],
OA [auth j],
QA [auth l],
TB [auth JA],
Y [auth T]
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-glucopyranose
BA [auth W],
HB [auth 3],
JA [auth e],
PB [auth FA],
RA [auth m],
BA [auth W],
HB [auth 3],
JA [auth e],
PB [auth FA],
RA [auth m],
ZA [auth u]
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-glucopyranose
CA [auth X],
IA [auth d],
IB [auth 4],
OB [auth EA],
SA [auth n],
CA [auth X],
IA [auth d],
IB [auth 4],
OB [auth EA],
SA [auth n],
YA [auth t]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseDA [auth Y],
JB [auth 9],
TA [auth o]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC
Entity ID: 14
MoleculeChains Length2D Diagram GlycosylationD 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 a],
LB [auth BA],
VA [auth q]
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 15
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-glucopyranoseBB [auth w],
LA [auth g],
RB [auth HA]
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
AC [auth K]
BC [auth Q]
CC [auth Q]
UB [auth 2]
VB [auth A]
AC [auth K],
BC [auth Q],
CC [auth Q],
UB [auth 2],
VB [auth A],
WB [auth A],
XB [auth B],
YB [auth G],
ZB [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2

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: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • 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: 2024-11-06
    Changes: Data collection, Database references, Refinement description, Structure summary