7L87

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.32034 (Wk26 time point)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM.

Antanasijevic, A.Sewall, L.M.Cottrell, C.A.Carnathan, D.G.Jimenez, L.E.Ngo, J.T.Silverman, J.B.Groschel, B.Georgeson, E.Bhiman, J.Bastidas, R.LaBranche, C.Allen, J.D.Copps, J.Perrett, H.R.Rantalainen, K.Cannac, F.Yang, Y.R.de la Pena, A.T.Rocha, R.F.Berndsen, Z.T.Baker, D.King, N.P.Sanders, R.W.Moore, J.P.Crotty, S.Crispin, M.Montefiori, D.C.Burton, D.R.Schief, W.R.Silvestri, G.Ward, A.B.

(2021) Nat Commun 12: 4817-4817

  • DOI: https://doi.org/10.1038/s41467-021-25087-4
  • Primary Citation of Related Structures:  
    7L7T, 7L7U, 7L85, 7L86, 7L87, 7L88, 7L89, 7L8A, 7L8B, 7L8C, 7L8D, 7L8E, 7L8F, 7L8G, 7L8S, 7L8T, 7L8U, 7L8W, 7L8X, 7L8Y, 7L8Z, 7L90

  • PubMed Abstract: 

    Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.


  • Organizational Affiliation

    Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rh.32034 pAbC-2 - Heavy ChainA [auth H]121Macaca mulattaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rh.32034 pAbC-2 - Light ChainB [auth L]103Macaca mulattaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BG505 SOSIP MD39 - gp120C,
E [auth A],
G [auth D]
498Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BG505 SOSIP MD39 - gp41D [auth E],
F [auth B],
H [auth F]
146Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
FA [auth f],
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
FA [auth f],
GA [auth g],
HA [auth h],
I [auth G],
IA [auth i],
J [auth I],
JA [auth j],
K [auth J],
KA [auth k],
L [auth K],
LA [auth l],
N,
NA [auth n],
O,
OA [auth o],
P,
PA [auth p],
R,
RA [auth r],
S,
SA [auth s],
T,
TA [auth t],
U,
UA [auth u],
V,
W,
X,
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranose
M
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
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-glucopyranoseDA [auth d],
Q,
QA [auth q]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseMA [auth m],
Z
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 B]
EB [auth D]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth B],
EB [auth D],
FB [auth D],
GB [auth D],
HB [auth F],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth E],
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: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTRosettaEM
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International AIDS Vaccine InitiativeUnited StatesOPP1196345

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 2.0: 2021-11-24
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Refinement description, Structure summary