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- EMDB-21254: Designed Nanoparticle Elicit Cross-Reactive Antibody Responses To... -

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Basic information

Entry
Database: EMDB / ID: EMD-21254
TitleDesigned Nanoparticle Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes
Map dataH1 nanoparticle
Sample
  • Virus: Hepatitis B virus
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsHarris AK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI001180 United States
CitationJournal: Biorxiv / Year: 2021
Title: Designed Nanoparticles Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes
Authors: McCraw DM / Myers ML / Gulati NM / Gallagher JR / Kim AJ / Torian U / Harris AK
History
DepositionJan 29, 2020-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 10, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0104
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0104
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21254.png

Downloads & links

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Map

FileDownload / File: emd_21254.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1 nanoparticle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 400 pix.
= 551.88 Å		1.38 Å/pix.
x 400 pix.
= 551.88 Å		1.38 Å/pix.
x 400 pix.
= 551.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3797 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0104 / Movie #1: 0.0104
Minimum - Maximum-0.00954405 - 0.06890957
Average (Standard dev.)0.003144612 (±0.008496433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 551.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.37971.37971.3797
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z551.880551.880551.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0100.0690.003

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Supplemental data

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Sample components

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Entire : Hepatitis B virus

EntireName: Hepatitis B virus
Components
  • Virus: Hepatitis B virus

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Details: Purified from bacteria / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Name: hbv capsid / Diameter: 300.0 Å / T number (triangulation number): 4

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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

Concentration1 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 83621
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 21485
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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