9BE9 | pdb_00009be9

HIV-1 Env 16055 dGly4 NFL


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9BE9

This is version 1.0 of the entry. See complete history

Literature

Accelerated cGMP production of near-native HIV-1 Env trimers following electroporation transfection and immunogenicity analysis.

Bale, S.Gustchina, E.Guenaga, J.Ayala, V.Lee, W.H.Ozorowski, G.Whitney, S.Wilson, R.Baboo, S.Diedrich, J.K.Doyle, E.D.Hudacik, L.Ben-Akiva, E.Rodrigues, K.A.Irvine, D.J.Yates 3rd, J.R.Paulson, J.C.Ward, A.B.Fouts, T.Wyatt, R.T.

(2025) NPJ Vaccines 10: 198-198

  • DOI: https://doi.org/10.1038/s41541-025-01218-6
  • Primary Citation Related Structures: 
    9BE9

  • PubMed Abstract: 

    Evaluation of recombinant HIV-1 surface glycoproteins (Env) as vaccine candidates for Phase I human experimental trials often requires production of cGMP-grade well-ordered Env trimers. Here, we report an accelerated cGMP compatible approach for expression and purification of a stabilized HIV clade C-derived trimer '16055 DG4 NFL' (for native flexibly linked). This recombinant trimer was expressed from CHO-S™ cells using a MaxCyte® VLX™ electroporation-based transient transfection process. The 16055 DG4 NFL was designed with multiple internal stabilizing mutations and, as well, deletion of four N-linked glycans (DG4) proximal to the CD4 binding site (CD4bs) engineered to improve B cell recognition of this conserved neutralizing determinant. The transient process circumvents the need to develop stable cell lines expressing the Env trimers that is often the most time-consuming step impacting vaccine development timelines. The 16055 DG4 NFL trimer was purified by immunoaffinity chromatography using the broadly neutralizing antibody (bNAb), PGT145. Following additional downstream processing steps, purified trimer was vialed, frozen and stored at -80 °C. Upon thaw and analysis, the trimer displayed homogeneity and a near-native conformation as determined by size-exclusion chromatography (SEC), negative stain and cryo-electron microscopy (EM), differential scanning calorimetry (DSC) and biolayer interferometry (BLI). The immunogenicity of the trimer was tested in rabbits with bolus, escalating dose and divided dose immunization regimens. Rabbits from all three regimens elicited tier 2 autologous neutralizing antibodies that targeted the exposed protein region at the CD4bs. The trimer is currently under investigation in a human clinical trial (NCT06332339) for safety, tolerability and as a priming candidate followed by heterologous boosting to potentially elicit cross-neutralizing antibodies.


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

Macromolecule Content 

  • Total Structure Weight: 229.86 kDa 
  • Atom Count: 14,253 
  • Modeled Residue Count: 1,656 
  • Deposited Residue Count: 1,914 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp140
A, B, C
638Human immunodeficiency virus 1Mutation(s): 26 
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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranose
G, M, S
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
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: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
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 StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release