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- EMDB-28542: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused ... -

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Basic information

Entry
Database: EMDB / ID: EMD-28542
TitleBG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
Map dataBG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Main Map
Sample
  • Complex: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
    • Protein or peptide: BG505 UFO-10GS-I3-01v9-L7P
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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_28542.png

Downloads & links

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Map

FileDownload / File: emd_28542.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Main Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 520 pix.
= 598. Å		1.15 Å/pix.
x 520 pix.
= 598. Å		1.15 Å/pix.
x 520 pix.
= 598. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018077927 - 0.046464816
Average (Standard dev.)-2.9410357e-05 (±0.001985185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 598.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28542_msk_1.map
Projections & Slices
AxesZYX

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Half map: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with...

Fileemd_28542_half_map_1.map
AnnotationBG505 UFO-10GS-I3-01v9-L7P 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-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with...

Fileemd_28542_half_map_2.map
AnnotationBG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core - Half Map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused ...

EntireName: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
Components
  • Complex: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused refinement with a mask around the nanoparticle core
    • Protein or peptide: BG505 UFO-10GS-I3-01v9-L7P

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Supramolecule #1: BG505 UFO-10GS-I3-01v9-L7P nanoparticle reconstructed by focused ...

SupramoleculeName: BG505 UFO-10GS-I3-01v9-L7P 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-10GS-I3-01v9-L7P 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-10GS-I3-01v9-L7P

MacromoleculeName: BG505 UFO-10GS-I3-01v9-L7P / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSRAEN LWVTVYYGVP VWKDAETTLF CASDAKAYDT EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKLT PLCVTLQCTN VTNNITDDMR GELKNCSFNM TTELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSRAEN LWVTVYYGVP VWKDAETTLF CASDAKAYDT EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKLT PLCVTLQCTN VTNNITDDMR GELKNCSFNM TTELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NGTGPCPSVS TVQCTHGIKP VVSTQLLLNG SLAEEEVMIR SENITNNAKN ILVQFNTPVQ INCTRPNNNT RKSIRIGPGQ AFYATGDIIG DIRQAHCNVS KATWNETLGK VVKQLRKHFG NNTIIRFANS SGGDLEVTTH SFNCGGEFFY CNTSGLFNST WISNTSVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWRSELYK YKVVKIEPLG VAPTRCKRRV VGGGGGSGGG GSAVGIGAVF LGFLGAAGST MGAASMTLTV QARNLLSGNP DWLPDMTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGKL ICCTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA LDASGGGGSG GGGSMKMEEL FKKHKIVAVL RANSVEEAKM KALAVFVGGV HLIEITFTVP DADTVIKELS FLKELGAIIG AGTVTSVEQC RKAVESGAEF IVSPHLDEEI SQFCKEKGVF YMPGVMTPTE LVKAMKLGHT ILKLFPGEVV GPQFVKAMKG PFPNVKFVPT GGVNLDNVCE WFKAGVLAVG VGSALVKGTI AEVAAKAAAF VEKIRGCTEG GGGSSPAVDI GDRLDELEKA LEALSAEDGH DDVGQRLESL LRRWNSRRAD GSAKFVAAWT LKAAA

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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-HCl
150.0 mMSodium chlorideNaCl

Details: TBS buffer prepared from a 10X stock
GridModel: Quantifoil R2/1 / Material: COPPER / 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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 1200 / Average exposure time: 12.0 sec. / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
Particle selectionNumber selected: 4806 / Details: cryoSPARC template picker
Startup modelType of model: OTHER
Details: Map obtained from Ab initio reconstruction in cryoSPARC with application of symmetry
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 4806
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4zk7

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