8F9M

HIV Env germline targeting BG505_MD64_N332-GT5 SOSIP in complex with V3-glycan polyclonal Fab isolated from immunized wild type mice, and NHP monoclonal Fab RM20A3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies.

Xie, Z.Lin, Y.C.Steichen, J.M.Ozorowski, G.Kratochvil, S.Ray, R.Torres, J.L.Liguori, A.Kalyuzhniy, O.Wang, X.Warner, J.E.Weldon, S.R.Dale, G.A.Kirsch, K.H.Nair, U.Baboo, S.Georgeson, E.Adachi, Y.Kubitz, M.Jackson, A.M.Richey, S.T.Volk, R.M.Lee, J.H.Diedrich, J.K.Prum, T.Falcone, S.Himansu, S.Carfi, A.Yates 3rd, J.R.Paulson, J.C.Sok, D.Ward, A.B.Schief, W.R.Batista, F.D.

(2024) Science 384: eadk0582-eadk0582

  • DOI: https://doi.org/10.1126/science.adk0582
  • Primary Citation of Related Structures:  
    8F92, 8F9G, 8F9M, 8VFV

  • PubMed Abstract: 

    Germline-targeting (GT) HIV vaccine strategies are predicated on deriving broadly neutralizing antibodies (bnAbs) through multiple boost immunogens. However, as the recruitment of memory B cells (MBCs) to germinal centers (GCs) is inefficient and may be derailed by serum antibody-induced epitope masking, driving further B cell receptor (BCR) modification in GC-experienced B cells after boosting poses a challenge. Using humanized immunoglobulin knockin mice, we found that GT protein trimer immunogen N332-GT5 could prime inferred-germline precursors to the V3-glycan-targeted bnAb BG18 and that B cells primed by N332-GT5 were effectively boosted by either of two novel protein immunogens designed to have minimum cross-reactivity with the off-target V1-binding responses. The delivery of the prime and boost immunogens as messenger RNA lipid nanoparticles (mRNA-LNPs) generated long-lasting GCs, somatic hypermutation, and affinity maturation and may be an effective tool in HIV vaccine development.


  • Organizational Affiliation

    The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BG505_MD64_N332-GT5 gp120A,
E,
I [auth F]
481synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 13
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 Fab Heavy ChainB [auth C],
F [auth J],
J [auth K]
125Macaca mulattaMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 Fab Light ChainC [auth D],
G [auth M],
K [auth N]
128Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BG505_MD64_N332-GT5 gp41D [auth B],
H [auth G],
L [auth I]
162synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V3-glycan epitope polyclonal Fab heavy chainM [auth H]113Mus musculusMutation(s): 0 
Sequence Annotations
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V3-glycan epitope polyclonal Fab light chainN [auth L]110Mus musculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, P, R, S, U
O, P, R, S, U, V, W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
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
Q, T
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth F]
BA [auth A]
BB [auth F]
CA [auth A]
AA [auth A],
AB [auth F],
BA [auth A],
BB [auth F],
CA [auth A],
CB [auth F],
DA [auth A],
DB [auth F],
EA [auth A],
EB [auth F],
FA [auth A],
FB [auth F],
GA [auth A],
GB [auth F],
HA [auth B],
HB [auth F],
IA [auth B],
IB [auth F],
JA [auth B],
JB [auth F],
KA [auth E],
KB [auth I],
LA [auth E],
LB [auth I],
MA [auth E],
MB [auth I],
NA [auth E],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth G],
WA [auth G],
X [auth A],
XA [auth G],
Y [auth A],
YA [auth F],
Z [auth A],
ZA [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1115782/INV-002916
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesA1144462

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references