7LX2 | pdb_00007lx2

Cryo-EM structure of ConSOSL.UFO.664 (ConS) in complex with bNAb PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7LX2

This is version 1.3 of the entry. See complete history

Literature

Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens.

Martin, G.M.Russell, R.A.Mundsperger, P.Harris, S.Jovanoska, L.Trajano, L.F.Schiffner, T.Fabian, K.Tolazzi, M.Scarlatti, G.McFarlane, L.Cheeseman, H.Aldon, Y.Schermer, E.E.Breemen, M.Sliepen, K.Katinger, D.Kunert, R.Sanders, R.W.Shattock, R.Ward, A.B.Sattentau, Q.J.

(2023) NPJ Vaccines 8: 101-101

  • DOI: https://doi.org/10.1038/s41541-023-00696-w
  • Primary Citation Related Structures: 
    7LX2, 7LX3, 7LXM, 7LXN

  • PubMed Abstract: 

    Chemical cross-linking is used to stabilize protein structures with additional benefits of pathogen and toxin inactivation for vaccine use, but its use has been restricted by the potential for local or global structural distortion. This is of particular importance when the protein in question requires a high degree of structural conservation for inducing a biological outcome such as the elicitation of antibodies to conformationally sensitive epitopes. The HIV-1 envelope glycoprotein (Env) trimer is metastable and shifts between different conformational states, complicating its use as a vaccine antigen. Here we have used the hetero-bifunctional zero-length reagent 1-Ethyl-3-(3-Dimethylaminopropyl)-Carbodiimide (EDC) to cross-link two soluble Env trimers, selected well-folded trimer species using antibody affinity, and transferred this process to good manufacturing practice (GMP) for experimental medicine use. Cross-linking enhanced trimer stability to biophysical and enzyme attack. Cryo-EM analysis revealed that cross-linking retained the overall structure with root-mean-square deviations (RMSDs) between unmodified and cross-linked Env trimers of 0.4-0.5 Å. Despite this negligible distortion of global trimer structure, we identified individual inter-subunit, intra-subunit, and intra-protomer cross-links. Antigenicity and immunogenicity of the trimers were selectively modified by cross-linking, with cross-linked ConS retaining bnAb binding more consistently than ConM. Thus, the EDC cross-linking process improves trimer stability whilst maintaining protein folding, and is readily transferred to GMP, consistent with the more general use of this approach in protein-based vaccine design.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. gmartin@scripps.edu.

Macromolecule Content 

  • Total Structure Weight: 392.79 kDa 
  • Atom Count: 20,196 
  • Modeled Residue Count: 2,322 
  • Deposited Residue Count: 3,318 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Env glycoprotein gp160A,
D [auth B],
G [auth C]
658Human immunodeficiency virus 1Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 Fab light chainB [auth L],
E [auth M],
H [auth O]
213Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT122 Fab heavy chainC [auth H],
F [auth N],
I [auth P]
235Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
AA [auth a],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
GA [auth g],
IA [auth i],
J [auth D],
JA [auth j],
K [auth E],
L [auth F],
LA [auth l],
M [auth G],
MA [auth m],
N [auth I],
NA [auth n],
OA [auth o],
P [auth K],
PA [auth p],
Q,
R,
RA [auth r],
S,
SA [auth s],
TA [auth t],
U,
UA [auth u],
V,
WA [auth w],
X,
XA [auth x],
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-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],
O [auth J],
QA [auth q]
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G42984ZU
GlyCosmos: G42984ZU
GlyGen: G42984ZU
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseHA [auth h],
T,
VA [auth v]
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G68668TB
GlyCosmos: G68668TB
GlyGen: G68668TB
Entity ID: 7
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-glucopyranoseKA [auth k],
W,
YA [auth y]
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
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
EB [auth B]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth C],
KB [auth C],
LB [auth C],
MB [auth C],
NB [auth C],
ZA [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: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary