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- EMDB-0350: Induction of Potent Neutralizing Antibody Responses by a Designed... -

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Basic information

Entry
Database: EMDB / ID: EMD-0350
TitleInduction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus
Map dataDS-Cav1-I53-50 nanoparticle
Sample
  • Complex: DS-Cav1-I53-50 nanoparticle
    • Protein or peptide: Engineered respiratory syncytial virus F protein (DS-Cav-1) fused to the foldon and to the trimeric component of I53-50 (DS-Cav1-I53-50A)
    • Protein or peptide: Pentameric component of I53-50 (I53-50B)Pentamer
Biological speciesRespiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsMarcandalli J / Fiala B / Ols S / Perotti M / van der Schueren W / Snijder S / Hodge E / Benhaim M / Ravichandran R / Carter L ...Marcandalli J / Fiala B / Ols S / Perotti M / van der Schueren W / Snijder S / Hodge E / Benhaim M / Ravichandran R / Carter L / Sheffler W / Brunner L / Lawrenz M / Dubois P / Lanzavecchia A / Sallusto F / Lee KK / Veesler D / Correnti CE / Stewart LJ / Baker D / Lore K / Perez L / King NP
CitationJournal: Cell / Year: 2019
Title: Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus.
Authors: Jessica Marcandalli / Brooke Fiala / Sebastian Ols / Michela Perotti / Willem de van der Schueren / Joost Snijder / Edgar Hodge / Mark Benhaim / Rashmi Ravichandran / Lauren Carter / Will ...Authors: Jessica Marcandalli / Brooke Fiala / Sebastian Ols / Michela Perotti / Willem de van der Schueren / Joost Snijder / Edgar Hodge / Mark Benhaim / Rashmi Ravichandran / Lauren Carter / Will Sheffler / Livia Brunner / Maria Lawrenz / Patrice Dubois / Antonio Lanzavecchia / Federica Sallusto / Kelly K Lee / David Veesler / Colin E Correnti / Lance J Stewart / David Baker / Karin Loré / Laurent Perez / Neil P King /
Abstract: Respiratory syncytial virus (RSV) is a worldwide public health concern for which no vaccine is available. Elucidation of the prefusion structure of the RSV F glycoprotein and its identification as ...Respiratory syncytial virus (RSV) is a worldwide public health concern for which no vaccine is available. Elucidation of the prefusion structure of the RSV F glycoprotein and its identification as the main target of neutralizing antibodies have provided new opportunities for development of an effective vaccine. Here, we describe the structure-based design of a self-assembling protein nanoparticle presenting a prefusion-stabilized variant of the F glycoprotein trimer (DS-Cav1) in a repetitive array on the nanoparticle exterior. The two-component nature of the nanoparticle scaffold enabled the production of highly ordered, monodisperse immunogens that display DS-Cav1 at controllable density. In mice and nonhuman primates, the full-valency nanoparticle immunogen displaying 20 DS-Cav1 trimers induced neutralizing antibody responses ∼10-fold higher than trimeric DS-Cav1. These results motivate continued development of this promising nanoparticle RSV vaccine candidate and establish computationally designed two-component nanoparticles as a robust and customizable platform for structure-based vaccine design.
History
DepositionNov 23, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseMar 20, 2019-
UpdateMar 20, 2019-
Current statusMar 20, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0350.png

Downloads & links

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Map

FileDownload / File: emd_0350.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDS-Cav1-I53-50 nanoparticle
Voxel sizeX=Y=Z: 2.5 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.038507614 - 0.17572236
Average (Standard dev.)0.0013413099 (±0.01018412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z600.000600.000600.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0390.1760.001

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Supplemental data

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Sample components

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Entire : DS-Cav1-I53-50 nanoparticle

EntireName: DS-Cav1-I53-50 nanoparticle
Components
  • Complex: DS-Cav1-I53-50 nanoparticle
    • Protein or peptide: Engineered respiratory syncytial virus F protein (DS-Cav-1) fused to the foldon and to the trimeric component of I53-50 (DS-Cav1-I53-50A)
    • Protein or peptide: Pentameric component of I53-50 (I53-50B)Pentamer

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Supramolecule #1: DS-Cav1-I53-50 nanoparticle

SupramoleculeName: DS-Cav1-I53-50 nanoparticle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Engineered respiratory syncytial virus F protein (DS-Cav-1) fused...

MacromoleculeName: Engineered respiratory syncytial virus F protein (DS-Cav-1) fused to the foldon and to the trimeric component of I53-50 (DS-Cav1-I53-50A)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PATNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVCKVLHL EGEVNKIKSA ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PATNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVCKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTF KVLDLKNYID KQLLPILNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMC IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEVN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGVDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRGYI PEAPRDGQAY VRKDGEWVLL STFLGSGSHH HHHHHHGGSG GSGSEKAAKA EEAARKMEEL FKKHKIVAVL RANSVEEAIE KAVAVFAGGV HLIEITFTVP DADTVIKALS VLKEKGAIIG AGTVTSVEQC RKAVESGAEF IVSPHLDEEI SQFCKEKGVF YMPGVMTPTE LVKAMKLGHT ILKLFPGEVV GPQFVKAMKG PFPNVKFVPT GGVNLDNVCE WFKAGVLAVG VGSALVKGTP DEVREKAKAF VEKIRGCTE

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Macromolecule #2: Pentameric component of I53-50 (I53-50B)

MacromoleculeName: Pentameric component of I53-50 (I53-50B) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
SequenceString:
MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVINGMM NVQLNTGVPV LSAVLTPHNY DKSKAHTLLF LALFAVKGME AARACVEILA AREKIAAGSL EHHHHHH

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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

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Computationally designed model
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1200

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