7LXM

Cryo-EM structure of ConM SOSIP.v7 (ConM) in complex with bNAb PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env glycoprotein gp120A,
E [auth C],
I [auth E]
493Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env glycoprotein gp41B,
F [auth D],
J [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Fab heavy chainC [auth H],
G [auth N],
K [auth P]
235Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 Fab light chainD [auth L],
H [auth M],
L [auth O]
213Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-glucopyranoseAA [auth a],
M [auth G],
OA [auth o]
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G94734OT
GlyCosmos:  G94734OT
GlyGen:  G94734OT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DA [auth d],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DA [auth d],
EA [auth e],
FA [auth f],
HA [auth h],
MA [auth m],
N [auth I],
NA [auth n],
O [auth J],
P [auth K],
PA [auth p],
Q,
QA [auth q],
R,
RA [auth r],
SA [auth s],
T,
TA [auth t],
VA [auth v],
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseGA [auth g],
S,
UA [auth u]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G23799GS
GlyCosmos:  G23799GS
GlyGen:  G23799GS
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseIA [auth i],
U,
WA [auth w]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseJA [auth j],
V,
XA [auth x]
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
KA [auth k],
LA [auth l],
W,
X,
YA [auth y],
KA [auth k],
LA [auth l],
W,
X,
YA [auth y],
ZA [auth z]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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