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- PDB-8eqn: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinemen... -

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Basic information

Entry
Database: PDB / ID: 8eqn
TitleBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
ComponentsBG505 UFO-E2p-L4P
KeywordsVIRAL PROTEIN / glycoprotein / BG505 / UFO / vaccine design / nanoparticle / protein design
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAntanasijevic, A. / Zhang, Y.N. / Zhu, J. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeOPP1196345 United States
CitationJournal: Nat Commun / Year: 2023
Title: Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates.
Authors: Yi-Nan Zhang / Jennifer Paynter / Aleksandar Antanasijevic / Joel D Allen / Mor Eldad / Yi-Zong Lee / Jeffrey Copps / Maddy L Newby / Linling He / Deborah Chavez / Pat Frost / Anna Goodroe / ...Authors: Yi-Nan Zhang / Jennifer Paynter / Aleksandar Antanasijevic / Joel D Allen / Mor Eldad / Yi-Zong Lee / Jeffrey Copps / Maddy L Newby / Linling He / Deborah Chavez / Pat Frost / Anna Goodroe / John Dutton / Robert Lanford / Christopher Chen / Ian A Wilson / Max Crispin / Andrew B Ward / Jiang Zhu /
Abstract: Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native- ...Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
History
DepositionOct 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BG505 UFO-E2p-L4P


Theoretical massNumber of molelcules
Total (without water)109,3711
Polymers109,3711
Non-polymers00
Water00
1
A: BG505 UFO-E2p-L4P
x 60


Theoretical massNumber of molelcules
Total (without water)6,562,25160
Polymers6,562,25160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BG505 UFO-E2p-L4P
x 5


  • icosahedral pentamer
  • 547 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)546,8545
Polymers546,8545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: BG505 UFO-E2p-L4P
x 6


  • icosahedral 23 hexamer
  • 656 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)656,2256
Polymers656,2256
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein BG505 UFO-E2p-L4P


Mass: 109370.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)

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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: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
Type: COMPLEX
Details: The map was generated by focused refinement of the BG505 UFO-E2p-L4P nanoparticle dataset using a mask around the nanoparticle core (masking out the flexibly linked antigens).
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster) / Cell: ExpiCHO
Buffer solutionpH: 7.4 / Details: TBS buffer prepared from a 10X stock
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 4.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The nanoparticle was expressed in ExpiCHO cells and purified using a combination of immuno-affinity chromatography and SEC.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: Blotting time varied between 3 and 7 seconds.

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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 FIELD / Nominal magnification: 29000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 10.25 sec. / Electron dose: 50.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2300
Image scansMovie frames/image: 41 / Used frames/image: 1-41

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4RELION3CTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10RosettaEMmodel refinement
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
Image processingDetails: Frames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 17097 / Details: cryoSPARC template picker
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7672 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4ZK7

4zk7


Accession code: 4ZK7 / Source name: PDB / Type: experimental model

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