+Open data
-Basic information
Entry | Database: PDB / ID: 6ohy | ||||||||||||
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Title | Chimpanzee SIV Env trimeric ectodomain. | ||||||||||||
Components | (Envelope glycoprotein ...) x 2 | ||||||||||||
Keywords | VIRAL PROTEIN / HIV / Cimpanzee / SIV / Env / Envelope / gp120 / gp41 / trimer / glycoprotein / simian / immunodeficiency / virus / vaccine. | ||||||||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Simian immunodeficiency virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Pallesen, J. / Andrabi, R. / de Val, N. / Burton, D.R. / Ward, A.B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell Rep / Year: 2019 Title: The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template. Authors: Raiees Andrabi / Jesper Pallesen / Joel D Allen / Ge Song / Jinsong Zhang / Natalia de Val / Gavin Gegg / Katelyn Porter / Ching-Yao Su / Matthias Pauthner / Amanda Newman / Hilary Bouton- ...Authors: Raiees Andrabi / Jesper Pallesen / Joel D Allen / Ge Song / Jinsong Zhang / Natalia de Val / Gavin Gegg / Katelyn Porter / Ching-Yao Su / Matthias Pauthner / Amanda Newman / Hilary Bouton-Verville / Fernando Garces / Ian A Wilson / Max Crispin / Beatrice H Hahn / Barton F Haynes / Laurent Verkoczy / Andrew B Ward / Dennis R Burton / 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) ...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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ohy.cif.gz | 344.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ohy.ent.gz | 289.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ohy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ohy_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 6ohy_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 6ohy_validation.xml.gz | 65.8 KB | Display | |
Data in CIF | 6ohy_validation.cif.gz | 96.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6ohy ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6ohy | HTTPS FTP |
-Related structure data
Related structure data | 20074MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 2 types, 6 molecules ACDBEF
#1: Protein | Mass: 51708.664 Da / Num. of mol.: 3 / Mutation: Q171K, A501C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q1A234 #2: Protein | Mass: 17179.490 Da / Num. of mol.: 3 / Mutation: I559P, D605C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q1A234 |
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-Sugars , 5 types, 66 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chimpanzee SIV Env trimeric ectodomain. / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.45 MDa / Experimental value: NO |
Source (natural) | Organism: Simian immunodeficiency virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 10 sec. / Electron dose: 94 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | |||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44301 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4TVP Accession code: 4TVP / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||
Refine LS restraints |
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