RCSB PDB - 9AXI: HIV 16055.v8.3 SOSIP Env in Complex with Base and N625 Epitope pAbs from Rabbit 2463

 9AXI

HIV 16055.v8.3 SOSIP Env in Complex with Base and N625 Epitope pAbs from Rabbit 2463


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.

Brown, S.Antanasijevic, A.Sewall, L.M.Garcia, D.M.Brouwer, P.J.M.Sanders, R.W.Ward, A.B.

(2025) Sci Immunol 10: eadp5218-eadp5218

  • DOI: https://doi.org/10.1126/sciimmunol.adp5218
  • Primary Citation of Related Structures:  
    9ATZ, 9AXD, 9AXI, 9AXK, 9AY6, 9AYS, 9AYV

  • PubMed Abstract: 

    Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.


  • Organizational Affiliation

    Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp41A [auth M],
B [auth D],
C [auth I]
155Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A0B5KUY7 (Human immunodeficiency virus type 1)
Explore A0A0B5KUY7 
Go to UniProtKB:  A0A0B5KUY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5KUY7
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody N625 Epitope - Predicted Light ChainD [auth F]110Oryctolagus cuniculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy ChainE [auth H]119Oryctolagus cuniculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy ChainF [auth A]122Oryctolagus cuniculusMutation(s): 0 
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody Base Epitope - Predicted Light ChainG [auth B]109Oryctolagus cuniculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Surface protein gp120H [auth K],
I [auth L],
J
514Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A1EAI1 (Human immunodeficiency virus type 1)
Explore A1EAI1 
Go to UniProtKB:  A1EAI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAI1
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 8
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-glucopyranoseBA [auth b],
M [auth G]
5N-Glycosylation
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
R
2N-Glycosylation
Entity ID: 10
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
W
4N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth L]
BB [auth L]
DB [auth L]
EB [auth J]
FA [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
CB [auth L]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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
Bill & Melinda Gates FoundationUnited StatesUM1 AI100663

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release