8T49

MD65 N332-GT5 SOSIP in complex with RM_N332_03 Fab and RM20A3 Fab


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 1.1 of the entry. See complete history


Literature

Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates.

Steichen, J.M.Phung, I.Salcedo, E.Ozorowski, G.Willis, J.R.Baboo, S.Liguori, A.Cottrell, C.A.Torres, J.L.Madden, P.J.Ma, K.M.Sutton, H.J.Lee, J.H.Kalyuzhniy, O.Allen, J.D.Rodriguez, O.L.Adachi, Y.Mullen, T.M.Georgeson, E.Kubitz, M.Burns, A.Barman, S.Mopuri, R.Metz, A.Altheide, T.K.Diedrich, J.K.Saha, S.Shields, K.Schultze, S.E.Smith, M.L.Schiffner, T.Burton, D.R.Watson, C.T.Bosinger, S.E.Crispin, M.Yates 3rd, J.R.Paulson, J.C.Ward, A.B.Sok, D.Crotty, S.Schief, W.R.

(2024) Science 384: eadj8321-eadj8321

  • DOI: https://doi.org/10.1126/science.adj8321
  • Primary Citation of Related Structures:  
    8T49, 8T4A, 8T4B, 8T4D, 8T4K, 8T4L

  • PubMed Abstract: 

    Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.


  • Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MD65 N332-GT5 SOSIP gp120A,
G [auth E],
M [auth F]
481Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RM_N332_03 heavy chain FvB [auth H],
H [auth O],
N [auth P]
131Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RM_N332_03 light chain FvC [auth L],
I [auth Q],
O [auth R]
108Macaca mulattaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 heavy chain FvD [auth C],
J,
P [auth K]
125Macaca mulattaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 light chain FvE [auth D],
K [auth M],
Q [auth N]
128Macaca mulattaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
MD65 N332-GT5 SOSIP gp41F [auth B],
L [auth G],
R [auth I]
153Human immunodeficiency virus 1Mutation(s): 0 
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Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseAA [auth a],
S,
W
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
T,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
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-glucopyranoseCA [auth c],
U,
Y
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 10
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-glucopyranoseDA [auth d],
V,
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth E]
AC [auth I]
BB [auth E]
BC [auth I]
CB [auth E]
AB [auth E],
AC [auth I],
BB [auth E],
BC [auth I],
CB [auth E],
CC [auth I],
DB [auth E],
EA [auth A],
EB [auth E],
FA [auth A],
FB [auth E],
GA [auth A],
GB [auth E],
HA [auth A],
HB [auth E],
IA [auth A],
IB [auth E],
JA [auth A],
JB [auth G],
KA [auth A],
KB [auth G],
LA [auth A],
LB [auth G],
MA [auth A],
MB [auth F],
NA [auth A],
NB [auth F],
OA [auth A],
OB [auth F],
PA [auth A],
PB [auth F],
QA [auth A],
QB [auth F],
RA [auth A],
RB [auth F],
SA [auth B],
SB [auth F],
TA [auth B],
TB [auth F],
UA [auth B],
UB [auth F],
VA [auth E],
VB [auth F],
WA [auth E],
WB [auth F],
XA [auth E],
XB [auth F],
YA [auth E],
YB [auth F],
ZA [auth E],
ZB [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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 Al100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references