9PYD | pdb_00009pyd

Q12QBM-007 Fab in complex with HIV-1 Env BG505 NFL TD CC3+


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 9PYD

This is version 1.0 of the entry. See complete history

Literature

Vaccination generates broadly cross-neutralizing antibodies to the HIV Env apex.

Guenaga, J.Adori, M.Bale, S.Phulera, S.Zygouras, I.Schleich, F.A.Castro Dopico, X.Agrawal, S.Ota, M.Wilson, R.Cluff, J.Dzvelaia, T.Mandolesi, M.Lee, W.H.Walsh, A.A.Melo, M.B.Verkoczy, L.Irvine, D.J.Corcoran, M.Wilson, I.A.Carnathan, D.Silvestri, G.Ward, A.B.Ozorowski, G.Karlsson Hedestam, G.B.Wyatt, R.T.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10429-3
  • Primary Citation Related Structures: 
    9PY5, 9PYD, 9PYH, 9PYK, 9PYN, 9PYY, 9PZ2, 9PZ3

  • PubMed Abstract: 

    As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans 1 . Broadly neutralizing antibodies, although rare, can be isolated from people living with HIV, revealing conserved envelope glycoprotein (Env) sites as key targets for vaccine development 2-4 . One such target is the apex of the Env spike. Here we identify a vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display that resulted in the elicitation of cross-neutralizing HIV serum antibody responses in all trimer-liposome-immunized non-human primates. Critically, we isolated monoclonal antibodies from multiple macaques that cross-neutralize divergent HIV clinical isolates. High-resolution cryogenic electron microscopy structural analyses of monoclonal antibodies from four different macaques demonstrate that they target the Env trimer apex in a manner highly similar to that of the human-infection-elicited, apex-directed broadly neutralizing antibody PG9, representing a substantial advance in HIV vaccine development.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 279.88 kDa 
  • Atom Count: 15,767 
  • Modeled Residue Count: 1,896 
  • Deposited Residue Count: 2,416 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 NFL TD CC3+ gp140
A, B, C
655Human immunodeficiency virus 1Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Q12QBM-007 Fab heavy chainD [auth H]237Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Q12QBM-007 Fab light chainE [auth L]214Macaca mulattaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
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-glucopyranoseF [auth D],
K [auth J],
O
3N-Glycosylation
Entity ID: 5
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-glucopyranoseG [auth E],
M
4N-Glycosylation
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth F],
J [auth I],
L [auth K],
N
2N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseI [auth G]5N-Glycosylation

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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 REFINEMENTPHENIX1.21.2_5419
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 StatesP01 AI157299

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release