8F92 | pdb_00008f92

HIV Env BG505_MD39_B11 SOSIP boosting trimer in complex with B11_d77.7 mouse Fab and RM20A3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8F92

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 392.35 kDa 
  • Atom Count: 24,882 
  • Modeled Residue Count: 3,063 
  • Deposited Residue Count: 3,399 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505_MD39_B11 gp120A,
G [auth E],
M [auth F]
481Human immunodeficiency virusMutation(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: 15
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 Fab heavy chainB [auth C],
H [auth J],
N [auth K]
125Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 Fab light chainC [auth D],
I [auth M],
O [auth N]
128Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505_MD39_B11 gp41D [auth B],
J [auth G],
P [auth I]
162Human immunodeficiency virusMutation(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: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
B11_d77.7 Fab heavy chainE [auth H],
K [auth O],
Q [auth P]
130Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
B11_d77.7 Fab kappa light chainF [auth L],
L [auth Q],
R
107Mus musculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
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-glucopyranose
S, V, Y
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 8
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
T, W, Z
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
U,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

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 StatesUMI A1144462

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
  • Version 1.2: 2024-06-05
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary