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- EMDB-28541: BG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanopar... -

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Basic information

Entry
Database: EMDB / ID: EMD-28541
TitleBG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanoparticle by localized reconstruction
Map dataBG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanoparticle by localized reconstruction - Main Map
Sample
  • Complex: BG505 UFO map obtained by localized reconstruction
    • Protein or peptide: BG505 UFO-E2p-L4P - Antigenic portion
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 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_28541.png

Downloads & links

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Map

FileDownload / File: emd_28541.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanoparticle by localized reconstruction - Main Map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.037392925 - 0.0645801
Average (Standard dev.)0.00092151493 (±0.0041119438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P...

Fileemd_28541_half_map_1.map
AnnotationBG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanoparticle by localized reconstruction - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P...

Fileemd_28541_half_map_2.map
AnnotationBG505 UFO trimer map reconstructed from BG505 UFO-E2p-L4P nanoparticle by localized reconstruction - Half Map 2
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 map obtained by localized reconstruction

EntireName: BG505 UFO map obtained by localized reconstruction
Components
  • Complex: BG505 UFO map obtained by localized reconstruction
    • Protein or peptide: BG505 UFO-E2p-L4P - Antigenic portion

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Supramolecule #1: BG505 UFO map obtained by localized reconstruction

SupramoleculeName: BG505 UFO map obtained by localized reconstruction / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: The map was generated by localized reconstruction of the BG505 UFO part of the BG505 UFO-E2p-L4P nanoparticle dataset
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: BG505 UFO-E2p-L4P - Antigenic portion

MacromoleculeName: BG505 UFO-E2p-L4P - Antigenic portion / 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 LDASGAAAKP ATTEGEFPET REKMSGIRRA IAKAMVHSKH TAPHVTLMDE ADVTKLVAHR KKFKAIAAEK GIKLTFLPYV VKALVSALRE YPVLNTAIDD ETEEIIQKHY YNIGIAADTD RGLLVPVIKH ADRKPIFALA QEINELAEKA RDGKLTPGEM KGASCTITNI GSAGGQWFTP VINHPEVAIL GIGRIAEKPI VRDGEIVAAP MLALSLSFDH RMIDGATAQK ALNHIKRLLS DPELLLMGGG GSFSEEQKKA LDLAFYFDRR LTPEWRRYLS QRLGLNEEQI ERWFRRKEQQ IGWSHPQFEK 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-HClTris
150.0 mMSodium chlorideNaClSodium chloride

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 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: 153400 / Details: Scipion, symmetry expansion
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: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6726
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

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