6OHY

Chimpanzee SIV Env trimeric ectodomain.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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

The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template.

Andrabi, R.Pallesen, J.Allen, J.D.Song, G.Zhang, J.de Val, N.Gegg, G.Porter, K.Su, C.Y.Pauthner, M.Newman, A.Bouton-Verville, H.Garces, F.Wilson, I.A.Crispin, M.Hahn, B.H.Haynes, B.F.Verkoczy, L.Ward, A.B.Burton, D.R.

(2019) Cell Rep 27: 2426-2441.e6

  • DOI: 10.1016/j.celrep.2019.04.082
  • Primary Citation of Related Structures:  
    6OHY

  • PubMed Abstract: 
  • Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) envelope (Env) shares a single bnAb site, the variable loop 2 (V2)-apex, with HIV, suggesting its possible utility in an HIV immunization strategy ...

    Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) envelope (Env) shares a single bnAb site, the variable loop 2 (V2)-apex, with HIV, suggesting its possible utility in an HIV immunization strategy. Here, we generate a chimpanzee SIV Env trimer, MT145K, which displays selective binding to HIV V2-apex bnAbs and precursor versions, but no binding to other HIV specificities. We determine the structure of the MT145K trimer by cryo-EM and show that its architecture is remarkably similar to HIV Env. Immunization of an HIV V2-apex bnAb precursor Ab-expressing knockin mouse with the chimpanzee MT145K trimer induces HIV V2-specific neutralizing responses. Subsequent boosting with an HIV trimer cocktail induces responses that exhibit some virus cross-neutralization. Overall, the chimpanzee MT145K trimer behaves as expected from design both in vitro and in vivo and is an attractive potential component of a sequential immunization regimen to induce V2-apex bnAbs.


    Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02114, USA. Electronic address: burton@scripps.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A, C, E [auth D]457Simian immunodeficiency virusMutation(s): 1 
Gene Names: env
UniProt
Find proteins for Q1A234 (Simian immunodeficiency virus)
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Go to UniProtKB:  Q1A234
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B, D [auth E], F151Simian immunodeficiency virusMutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q1A234 (Simian immunodeficiency virus)
Explore Q1A234 
Go to UniProtKB:  Q1A234
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth c], G, GA [auth g], HA [auth h], IA [auth i], O, QA [auth q], S
CA [auth c], G, GA [auth g], HA [auth h], IA [auth i], O, QA [auth q], S, T, U, UA [auth u], VA [auth v]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a], DA [auth d], EA [auth e], FA [auth f], H, I, JA [auth j], K
AA [auth a], DA [auth d], EA [auth e], FA [auth f], H, I, JA [auth j], K, KA [auth k], L, M, MA [auth m], NA [auth n], OA [auth o], P, Q, R, RA [auth r], SA [auth s], TA [auth t], V, W, Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseJ, LA [auth l], X3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseBA [auth b], N, PA [auth p]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G97423PY
GlyCosmos:  G97423PY
GlyGen:  G97423PY
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] , BB [auth A] , CB [auth A] , DB [auth B] , EB [auth C] , FB [auth C] , GB [auth C] , HB [auth C] , 
AB [auth A],  BB [auth A],  CB [auth A],  DB [auth B],  EB [auth C],  FB [auth C],  GB [auth C],  HB [auth C],  IB [auth C],  JB [auth C],  KB [auth C],  LB [auth E],  MB [auth D],  NB [auth D],  OB [auth D],  PB [auth D],  QB [auth D],  RB [auth D],  SB [auth D],  TB [auth F],  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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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 StatesAI100663
Bill & Melinda Gates FoundationUnited StatesOPP115782
Bill & Melinda Gates FoundationUnited StatesOPP1084519

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary