9AYS | pdb_00009ays

HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with V5, gp120-Interface, and Anti-Immune Complex pAbs from Rh.33203


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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: 301 kDa 
  • Atom Count: 18,710 
  • Modeled Residue Count: 2,428 
  • Deposited Residue Count: 2,644 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP gp120-Interface Epitope pAb - Predicted Heavy ChainA [auth H]121Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP gp120-Interface Epitope pAb - Predicted Light ChainB [auth L]101Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Surface protein gp120C [auth A],
E [auth C],
G [auth E]
514Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
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: 19
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane protein gp41D [auth B],
F [auth D],
H [auth F]
155Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for D0PUM0 (Human immunodeficiency virus type 1)
Explore D0PUM0 
Go to UniProtKB:  D0PUM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0PUM0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP V5 Epitope pAb - Predicted Light ChainI [auth G]102Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP V5 Epitope pAb - Predicted Heavy ChainJ [auth I]115Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP Anti-Immune Complex pAb - Predicted Heavy ChainK [auth J]104Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NHP Anti-Immune Complex pAb - Predicted Light ChainL [auth K]94Macaca mulattaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, V
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G35932AR
GlyCosmos: G35932AR
GlyGen: G35932AR
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][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
Q
6N-Glycosylation
Entity ID: 13
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-glucopyranoseCA [auth c],
W
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 14
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G11411VI
GlyCosmos: G11411VI
GlyGen: G11411VI

Small Molecules

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

Query on NAG



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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 StatesINV-002916
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United 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