8SWV

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody IF1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 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

Priming antibody responses to the fusion peptide in rhesus macaques.

Cottrell, C.A.Pratap, P.P.Cirelli, K.M.Carnathan, D.G.Enemuo, C.A.Antanasijevic, A.Ozorowski, G.Sewall, L.M.Gao, H.Allen, J.D.Nogal, B.Silva, M.Bhiman, J.Pauthner, M.Irvine, D.J.Montefiori, D.Crispin, M.Burton, D.R.Silvestri, G.Crotty, S.Ward, A.B.

(2024) NPJ Vaccines 9: 126-126

  • DOI: https://doi.org/10.1038/s41541-024-00918-9
  • Primary Citation of Related Structures:  
    8SWV, 8SWW, 8SWX, 8T2E, 8T2F

  • PubMed Abstract: 

    Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to prime and elicit antibody responses against the conserved fusion peptide (FP). GC responses and antibody specificities were tracked longitudinally using lymph node fine-needle aspirates and electron microscopy polyclonal epitope mapping (EMPEM), respectively, to show antibody responses to the FP/N611 glycan hole region were primed, although exhibited limited neutralization breadth. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, 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
Surface protein gp120A,
D [auth E],
F
516Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp41B,
C,
E [auth D]
153Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IF1 Heavy ChainG [auth H]122Macaca mulattaMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
IF1 Light ChainH [auth L]105Macaca mulattaMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G],
K [auth J],
M,
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseJ [auth I],
L [auth K]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 7
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-glucopyranose
N
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 
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 B],
GA [auth B],
HA [auth B],
IA [auth C],
JA [auth C],
KA [auth E],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth E],
P [auth A],
PA [auth E],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
T [auth A],
TA [auth E],
U [auth A],
UA [auth E],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth D],
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: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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 StatesR01 AI136621
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1AI10066
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: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Database references