6U59

HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits.

Yang, Y.R.McCoy, L.E.van Gils, M.J.Andrabi, R.Turner, H.L.Yuan, M.Cottrell, C.A.Ozorowski, G.Voss, J.Pauthner, M.Polveroni, T.M.Messmer, T.Wilson, I.A.Sanders, R.W.Burton, D.R.Ward, A.B.

(2020) J Virol 94

  • DOI: 10.1128/JVI.01861-19
  • Primary Citation of Related Structures:  
    6U59

  • PubMed Abstract: 
  • Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of the heavily glycosylated trimer that lacks potential N-linked glycosylation sites at positions 230, 241, and 289 ...

    Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of the heavily glycosylated trimer that lacks potential N-linked glycosylation sites at positions 230, 241, and 289. The Env derived from B41, a subtype B virus, shares a glycan hole centered on positions 230 and 289. To test whether broader neutralization to the common glycan hole can be achieved, we immunized rabbits with B41 SOSIP (gp120-gp41 disulfide [SOS] with an isoleucine-to-proline mutation [IP] in gp41) alone, as well as B41 and BG505 coimmunization. We isolated autologous neutralizing antibodies (nAbs) and described their structure in complex with the B41 Env. Our data suggest that distinct autologous nAb lineages are induced by BG505 and B41 immunogens, even when both were administered together. In contrast to previously described BG505 glycan hole antibodies, the B41-specific nAbs accommodate the >97% conserved N241 glycan, which is present in B41. Single-particle cryo-electron microscopy studies confirmed that B41- and BG505-specific nAbs bind to overlapping glycan hole epitopes. We then used our high-resolution data to guide mutations in the BG505 glycan hole epitope in an attempt to broaden the reactivity of a B41-specific nAb, but we recovered only partial binding. Our data demonstrate that the lack of cross-reactivity in glycan hole antibodies is due to amino acid differences within the epitope, and our attempts to rationally design cross-reactive trimers resulted in only limited success. Thus, even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult. IMPORTANCE A glycan hole is one of the most dominant autologous neutralizing epitopes targeted on BG505 and B41 SOSIP trimer-immunized rabbits. Our high-resolution cryo-electron microscopy (cryoEM) studies of B41 in complex with a B41-specific antibody complex elucidate the molecular basis of this strain-specific glycan hole response. We conclude that even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult.


    Organizational Affiliation

    Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOSIP.664 gp120,SOSIP.664 gp120A, E [auth C], I [auth G]524Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: env
UniProt
Find proteins for B3UES2 (Human immunodeficiency virus 1)
Explore B3UES2 
Go to UniProtKB:  B3UES2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SOSIP.664 gp41B, F [auth D], J [auth I]153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for B3UEZ6 (Human immunodeficiency virus 1)
Explore B3UEZ6 
Go to UniProtKB:  B3UEZ6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
rabbit antibody 13B Fragment antigen binding light chainG [auth E], K [auth J], C [auth L]112Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
rabbit antibody 13B Fragment antigen binding heavy chainH [auth F], D [auth H], L [auth K]119Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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], DA [auth d], FA [auth f], GA [auth g], HA [auth h], IA [auth i]
AA [auth a], BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], HA [auth h], IA [auth i], KA [auth k], LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], X, XA [auth x], Y, YA [auth y], Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e], R, RA [auth r]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseJA [auth j], W, WA [auth w]4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A] , AC [auth I] , BB [auth A] , BC [auth I] , CB [auth A] , CC [auth I] , DB [auth A] , EB [auth A] , 
AB [auth A],  AC [auth I],  BB [auth A],  BC [auth I],  CB [auth A],  CC [auth I],  DB [auth A],  EB [auth A],  FB [auth B],  GB [auth B],  HB [auth B],  IB [auth B],  JB [auth C],  KB [auth C],  LB [auth C],  MB [auth C],  NB [auth C],  OB [auth C],  PB [auth D],  QB [auth D],  RB [auth D],  SB [auth D],  TB [auth G],  UB [auth G],  VB [auth G],  WB [auth G],  XB [auth G],  YB [auth G],  ZA [auth A],  ZB [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-27 
  • Released Date: 2020-01-29 
  • Deposition Author(s): Yang, Y.R., Ward, A.B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1AI100663
Bill & Melinda Gates FoundationUnited StatesOPP1115782
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary