9AXI | pdb_00009axi

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

Validation slider image for 9AXI

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 283.67 kDa 
  • Atom Count: 17,031 
  • Modeled Residue Count: 2,164 
  • Deposited Residue Count: 2,467 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
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 A0A866DY39 (Human immunodeficiency virus type 1)
Explore A0A866DY39 
Go to UniProtKB:  A0A866DY39
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A866DY39
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody N625 Epitope - Predicted Light ChainD [auth F]110Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy ChainE [auth H]119Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy ChainF [auth A]122Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit Polyclonal Antibody Base Epitope - Predicted Light ChainG [auth B]109Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
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: 15
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD 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
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
R
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G35932AR
GlyCosmos: G35932AR
GlyGen: G35932AR
Entity ID: 10
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
W
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

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]
AB [auth L],
BB [auth L],
DB [auth L],
EB [auth J],
FA [auth M],
FB [auth J],
GA [auth M],
GB [auth J],
HA [auth M],
HB [auth J],
IA [auth M],
IB [auth J],
JA [auth D],
JB [auth J],
KA [auth I],
KB [auth J],
LA [auth I],
LB [auth J],
MA [auth I],
MB [auth J],
NA [auth K],
OA [auth K],
PA [auth K],
QA [auth K],
RA [auth K],
SA [auth K],
TA [auth K],
UA [auth K],
VA [auth K],
WA [auth L],
XA [auth L],
YA [auth L],
ZA [auth L]
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
MODEL REFINEMENTPHENIX
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
  • Version 1.1: 2025-05-14
    Changes: Data collection