8TGU | pdb_00008tgu

Cryo-EM structure of BG505 SOSIP trimer purified via Galanthus nivalis lectin chromatography


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8TGU

This is version 1.2 of the entry. See complete history

Literature

Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies.

Parthasarathy, D.Pothula, K.R.Ratnapriya, S.Cervera Benet, H.Parsons, R.Huang, X.Sammour, S.Janowska, K.Harris, M.Sodroski, J.Acharya, P.Herschhorn, A.

(2024) Nat Commun 15: 7334-7334

  • DOI: https://doi.org/10.1038/s41467-024-51656-4
  • Primary Citation Related Structures: 
    8TGU, 8TGW

  • PubMed Abstract: 

    HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed conformation and infrequently sample open states, limiting access to internal epitopes. Thus, immunogen design aims to mimic the closed Env conformation as preferred target for eliciting broadly neutralizing antibodies (bnAbs). Here we identify incompletely closed Env conformations of 6 out of 13 transmitted/founder (T/F) strains that are sensitive to antibodies that recognize internal epitopes typically exposed on open Envs. A 3.6 Å cryo-electron microscopy structure of unliganded, incompletely closed T/F Envs (1059-SOSIP) reveals protomer motion that increased sampling of states with incompletely closed trimer apex. We reconstruct de novo the post-transmission evolutionary pathway of a second T/F. Evolved viruses exhibit increased Env resistance to cold, soluble CD4 and 19b, all of which correlate with closing of the adapted Env trimer. Lastly, we show that the ultra-broad N6 bnAb efficiently recognizes different Env conformations and exhibits improved antiviral breadth against VRC01-resistant Envs isolated during the first-in-humans antibody-mediated-prevention trial.


  • Organizational Affiliation
    • Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.

Macromolecule Content 

  • Total Structure Weight: 233.01 kDa 
  • Atom Count: 14,880 
  • Modeled Residue Count: 1,719 
  • Deposited Residue Count: 1,893 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 Envelope glycoprotein BG505 SOSIP
A, B, C
631Human immunodeficiency virus 1Mutation(s): 0 
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: 15
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
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-glucopyranoseDA [auth d],
G,
K,
O,
P
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
S
2N/A
Glycosylation Resources
GlyTouCan: G90333CG
GlyCosmos: G90333CG
GlyGen: G90333CG

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],
IB [auth C],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
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 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI145687
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI170752
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU01 AI169587

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary