6OHY | pdb_00006ohy

Chimpanzee SIV Env trimeric ectodomain.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 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: https://doi.org/10.1016/j.celrep.2019.04.082
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 231.98 kDa 
  • Atom Count: 15,192 
  • Modeled Residue Count: 1,701 
  • Deposited Residue Count: 1,824 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A,
C,
E [auth D]
457Simian immunodeficiency virusMutation(s): 1 
Gene Names: env
UniProt
Find proteins for Q1A234 (Simian immunodeficiency virus)
Explore Q1A234 
Go to UniProtKB:  Q1A234
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1A234
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B,
D [auth E],
F
151Simian immunodeficiency virusMutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q1A234 (Simian immunodeficiency virus)
Explore Q1A234 
Go to UniProtKB:  Q1A234
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1A234
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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],
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
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD 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],
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD 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
Glycosylation Resources
GlyTouCan: G97423PY
GlyCosmos: G97423PY
GlyGen: G97423PY

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 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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary