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- EMDB-28540: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinemen... -

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Basic information

Entry
Database: EMDB / ID: EMD-28540
TitleBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
Map dataBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Main Map
Sample
  • Complex: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
    • Protein or peptide: BG505 UFO-E2p-L4P
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAntanasijevic A / Zhang YN / Zhu J / Ward AB
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28540.png

Downloads & links

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Map

FileDownload / File: emd_28540.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Main Map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.030455876 - 0.054780617
Average (Standard dev.)0.000115133254 (±0.0021627948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 535.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28540_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with...

Fileemd_28540_half_map_1.map
AnnotationBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with...

Fileemd_28540_half_map_2.map
AnnotationBG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinemen...

EntireName: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
Components
  • Complex: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
    • Protein or peptide: BG505 UFO-E2p-L4P

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Supramolecule #1: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinemen...

SupramoleculeName: BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
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).
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: BG505 UFO-E2p-L4P

MacromoleculeName: BG505 UFO-E2p-L4P / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 109.370852 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSRAEN LWVTVYYGVP VWKDAETTLF CASDAKAYDT EKHNVWATHA CVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN M TTELRDKK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSRAEN LWVTVYYGVP VWKDAETTLF CASDAKAYDT EKHNVWATHA CVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN M TTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY RLINCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCKDK KF NGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MIRSENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQ AFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHFGNNTIIR FANSSGGDLE VTTHSFNCGG EFFYCNTSGL FNST WISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDM RDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGGG GGSGGGGSAV GIGAVFLGFL GAAGSTMGAA SMTLTVQARN LLSGNP DWL PDMTVWGIKQ LQARVLAVER YLRDQQLLGI WGCSGKLICC TNVPWNSSWS NRNLSEIWDN MTWLQWDKEI SNYTQII YG LLEESQNQQE KNEQDLLALD ASGAAAKPAT TEGEFPETRE KMSGIRRAIA KAMVHSKHTA PHVTLMDEAD VTKLVAHR K KFKAIAAEKG IKLTFLPYVV KALVSALREY PVLNTSIDDE TEEIIQKHYY NIGIAADTDR GLLVPVIKHA DRKPIFALA QEINELAEKA RDGKLTPGEM KGASCTITNI GSAGGQWFTP VINHPEVAIL GIGRIAEKPI VRDGEIVAAP MLALSLSFDH RMIDGATAQ KALNHIKRLL SDPELLLMGG GGSFSEEQKK ALDLAFYFDR RLTPEWRRYL SQRLGLNEEQ IERWFRRKEQ Q IGWSHPQF EKGSAKFVAA WTLKAAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
150.0 mMSodium chlorideNaClSodium chloride

Details: TBS buffer prepared from a 10X stock
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time varied between 3 and 7 seconds..
DetailsThe nanoparticle was expressed in ExpiCHO cells and purified using a combination of immuno-affinity chromatography and SEC.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-41 / Number grids imaged: 1 / Number real images: 2300 / Average exposure time: 10.25 sec. / Average electron dose: 50.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 17097 / Details: cryoSPARC template picker
Startup modelType of model: OTHER
Details: Map obtained from Ab initio reconstruction in cryoSPARC with application of symmetry
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7672
DetailsFrames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4zk7

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8eqn:
BG505 UFO-E2p-L4P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core

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