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- PDB-6ohy: Chimpanzee SIV Env trimeric ectodomain. -

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Entry
Database: PDB / ID: 6ohy
TitleChimpanzee SIV Env trimeric ectodomain.
Components(Envelope glycoprotein ...) x 2
KeywordsVIRAL 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 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane
Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Gp120 core superfamily / Envelope glycoprotein GP120 / Retroviral envelope protein
Envelope glycoprotein gp160
Biological speciesSimian immunodeficiency virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPallesen, J. / Andrabi, R. / de Val, N. / Burton, D.R. / Ward, A.B.
Funding supportUnited States , 3件
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI100663United States
Bill & Melinda Gates FoundationOPP115782United States
Bill & Melinda Gates FoundationOPP1084519United States
CitationJournal: 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-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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 8, 2019 / Release: Jun 5, 2019
RevisionDateData content typeProviderType
1.0Jun 5, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
E: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
F: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,065132
Polymers206,6646
Non-polymers26,401126
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules ACDBEF

#1: Protein/peptide Envelope glycoprotein gp160


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/peptide Envelope glycoprotein gp160


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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Non-polymers , 4 types, 126 molecules

#3: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 96
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical
ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chimpanzee SIV Env trimeric ectodomain. / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)Organism: Simian immunodeficiency virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 sec. / Electron dose: 94 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
1DoG Pickerparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13Rosettamodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44301 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 4TVP
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00615630
f_angle_d1.08121486
f_dihedral_angle_d6.3719123
f_chiral_restr0.0622751
f_plane_restr0.0072574

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