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- EMDB-11398: I5350 negative staining -

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Basic information

Entry
Database: EMDB / ID: EMD-11398
TitleI5350 negative staining
Map dataI5350 Nanoparticle
Sample
  • Complex: 53-50A in complex with I53-50B.4PT1
    • Protein or peptide: I5350
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPerez L
CitationJournal: PLoS Pathog / Year: 2020
Title: Rationally designed Human Cytomegalovirus gB nanoparticle vaccine with improved immunogenicity.
Authors: Michela Perotti / Jessica Marcandalli / Davide Demurtas / Federica Sallusto / Laurent Perez /
Abstract: Human cytomegalovirus (HCMV) is the primary viral cause of congenital birth defects and causes significant morbidity and mortality in immune-suppressed transplant recipients. Despite considerable ...Human cytomegalovirus (HCMV) is the primary viral cause of congenital birth defects and causes significant morbidity and mortality in immune-suppressed transplant recipients. Despite considerable efforts in vaccine development, HCMV infection still represents an unmet clinical need. In recent phase II trials, a MF59-adjuvanted gB vaccine showed only modest efficacy in preventing infection. These findings might be attributed to low level of antibodies (Abs) with a neutralizing activity induced by this vaccine. Here, we analyzed the immunogenicity of each gB antigenic domain (AD) and demonstrated that domain I of gB (AD5) is the main target of HCMV neutralizing antibodies. Furthermore, we designed, characterized and evaluated immunogenic responses to two different nanoparticles displaying a trimeric AD5 antigen. We showed that mice immunization with nanoparticles induces sera neutralization titers up to 100-fold higher compared to those obtained with the gB extracellular domain (gBECD). Collectively, these results illustrate with a medically relevant example the advantages of using a general approach combining antigen discovery, protein engineering and scaffold presentation for modern development of subunit vaccines against complex pathogens.
History
DepositionJul 16, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11398.png

Downloads & links

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Map

FileDownload / File: emd_11398.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationI5350 Nanoparticle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 400 pix.
= 825. Å		2.06 Å/pix.
x 400 pix.
= 825. Å		2.06 Å/pix.
x 400 pix.
= 825. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.0625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.5138967 - 5.796297
Average (Standard dev.)-0.013847562 (±0.38873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 825.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.06252.06252.0625
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z825.000825.000825.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.5145.796-0.014

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Supplemental data

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Sample components

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Entire : 53-50A in complex with I53-50B.4PT1

EntireName: 53-50A in complex with I53-50B.4PT1
Components
  • Complex: 53-50A in complex with I53-50B.4PT1
    • Protein or peptide: I5350

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Supramolecule #1: 53-50A in complex with I53-50B.4PT1

SupramoleculeName: 53-50A in complex with I53-50B.4PT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: I5350

MacromoleculeName: I5350 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKMEELFKKH KIVAVLRANS VEEAIEKAVA VFAGGVHLIE ITFTVPDADT VIKALSVLKE KGAIIGAGTV TSVEQCRKAV ESGAEFIVSP HLDEEISQFC KEKGVFYMPG VMTPTELVKA MKLGHTILKL FPGEVVGPQF VKAMKGPFPN VKFVPTGGV NLDNVCEWFK ...String:
MKMEELFKKH KIVAVLRANS VEEAIEKAVA VFAGGVHLIE ITFTVPDADT VIKALSVLKE KGAIIGAGTV TSVEQCRKAV ESGAEFIVSP HLDEEISQFC KEKGVFYMPG VMTPTELVKA MKLGHTILKL FPGEVVGPQF VKAMKGPFPN VKFVPTGGV NLDNVCEWFK AGVLAVGVGS ALVKGTPDEV REKAKAFVEK IRGCTELEHH HHHH MNQHS HKDHETVRIA VVRARWHAEI VDACVSAFEA AMRDIGGDRF AVDVFDVPGA YEIPLHARTL AETGRYGAVL GT AFVVNGG IYRHEFVASA VINGMMNVQL NTGVPVLSAV LTPHNYDKSK AHTLLFLALF AVKGMEAARA CVEILAAREK I AAGSLEHH HHHH

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7
StainingType: NEGATIVE / Material: uranyl acetate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.26 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 8467
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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