6VL5 | pdb_00006vl5

BG505 SOSIP reconstructed from a designed tetrahedral nanoparticle, BG505 SOSIP-T33_dn2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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 6VL5

This is version 1.2 of the entry. See complete history

Literature

Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations.

Martin, J.T.Cottrell, C.A.Antanasijevic, A.Carnathan, D.G.Cossette, B.J.Enemuo, C.A.Gebru, E.H.Choe, Y.Viviano, F.Fischinger, S.Tokatlian, T.Cirelli, K.M.Ueda, G.Copps, J.Schiffner, T.Menis, S.Alter, G.Schief, W.R.Crotty, S.King, N.P.Baker, D.Silvestri, G.Ward, A.B.Irvine, D.J.

(2020) NPJ Vaccines 5: 72-72

  • DOI: https://doi.org/10.1038/s41541-020-00223-1
  • Primary Citation Related Structures: 
    6VKN, 6VL5, 6VL6

  • PubMed Abstract: 

    Following immunization, high-affinity antibody responses develop within germinal centers (GCs), specialized sites within follicles of the lymph node (LN) where B cells proliferate and undergo somatic hypermutation. Antigen availability within GCs is important, as B cells must acquire and present antigen to follicular helper T cells to drive this process. However, recombinant protein immunogens such as soluble human immunodeficiency virus (HIV) envelope (Env) trimers do not efficiently accumulate in follicles following traditional immunization. Here, we demonstrate two strategies to concentrate HIV Env immunogens in follicles, via the formation of immune complexes (ICs) or by employing self-assembling protein nanoparticles for multivalent display of Env antigens. Using rhesus macaques, we show that within a few days following immunization, free trimers were present in a diffuse pattern in draining LNs, while trimer ICs and Env nanoparticles accumulated in B cell follicles. Whole LN imaging strikingly revealed that ICs and trimer nanoparticles concentrated in as many as 500 follicles in a single LN within two days after immunization. Imaging of LNs collected seven days postimmunization showed that Env nanoparticles persisted on follicular dendritic cells in the light zone of nascent GCs. These findings suggest that the form of antigen administered in vaccination can dramatically impact localization in lymphoid tissues and provides a new rationale for the enhanced immune responses observed following immunization with ICs or nanoparticles.


  • Organizational Affiliation
    • Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.

Macromolecule Content 

  • Total Structure Weight: 249.49 kDa 
  • Atom Count: 15,039 
  • Modeled Residue Count: 1,719 
  • Deposited Residue Count: 2,016 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 SOSIP.v5.2(7S) - gp120A [auth C],
C [auth A],
E
506synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 SOSIP.v5.2(7S) - gp41B [auth D],
D [auth B],
F
166synthetic 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 A]
BB [auth A]
CB [auth A]
DB [auth A]
EB [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth E],
JB [auth E],
KA [auth C],
KB [auth E],
LA [auth C],
LB [auth E],
MA [auth C],
MB [auth E],
NA [auth C],
NB [auth E],
OA [auth C],
OB [auth E],
PA [auth C],
PB [auth E],
QA [auth C],
QB [auth E],
RA [auth C],
RB [auth F],
SA [auth C],
SB [auth F],
TA [auth D],
TB [auth F],
UA [auth D],
VA [auth D],
WA [auth A],
XA [auth A],
YA [auth A],
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: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta
MODEL REFINEMENTCoot

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: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary