6VFL | pdb_00006vfl

BG505-SOSIP model reconstructed by subparticle extraction and refinement from a tetrahedral nanoparticle T33_dn10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 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 6VFL

This is version 2.2 of the entry. See complete history

Literature

Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens.

Antanasijevic, A.Ueda, G.Brouwer, P.J.M.Copps, J.Huang, D.Allen, J.D.Cottrell, C.A.Yasmeen, A.Sewall, L.M.Bontjer, I.Ketas, T.J.Turner, H.L.Berndsen, Z.T.Montefiori, D.C.Klasse, P.J.Crispin, M.Nemazee, D.Moore, J.P.Sanders, R.W.King, N.P.Baker, D.Ward, A.B.

(2020) PLoS Pathog 16: e1008665-e1008665

  • DOI: https://doi.org/10.1371/journal.ppat.1008665
  • Primary Citation Related Structures: 
    6VFK, 6VFL

  • PubMed Abstract: 

    Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and geometries enables combination with antigens of choice to test novel multimerization concepts in immunization strategies where the goal is to improve the induction and maturation of neutralizing antibody lineages. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to an underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. When the immunogenicity of ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle or as soluble proteins were compared in rabbits, the two immunogens elicited similar serum antibody binding titers against the trimer component. Neutralizing antibody titers were slightly elevated in the animals given the nanoparticle immunogen and were initially more focused to the trimer apex. Altogether, our findings indicate that tetrahedral nanoparticles can be successfully applied for presentation of HIV Env trimer immunogens; however, the optimal implementation to different immunization strategies remains to be determined.


  • Organizational Affiliation
    • Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America.

Macromolecule Content 

  • Total Structure Weight: 243.68 kDa 
  • Atom Count: 14,925 
  • Modeled Residue Count: 1,710 
  • Deposited Residue Count: 1,980 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505-SOSIPv5.2(7S) - gp120
A, C, E
507synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505-SOSIPv5.2(7S) - gp41
B, D, F
153synthetic constructMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
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-glucopyranoseAA [auth a],
G,
Q
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

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 D]
EB [auth D]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth D],
EB [auth D],
FB [auth D],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KA [auth A],
KB [auth E],
LA [auth A],
LB [auth E],
MA [auth A],
MB [auth E],
NA [auth A],
NB [auth E],
OA [auth A],
OB [auth F],
PA [auth A],
PB [auth F],
QA [auth A],
QB [auth F],
RA [auth A],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-26
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary