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- EMDB-27057: Structures of Zika Virus in Complex with Antibodies Targeting E D... -

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Basic information

Entry
Database: EMDB / ID: EMD-27057
TitleStructures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy
Map data
Sample
  • Virus: Zika virus
KeywordsZIKV / scFv antibody / VIRUS / VIRUS-IMMUNE SYSTEM complex
Biological speciesZika virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu W / Zhang XK / Gong DY / Dai XH / Sharma A / Zhang TH / Rey F / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: To Be Published
Title: Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy
Authors: Liu W / Zhang XK / Gong DY / Dai XH / Sharma A / Zhang TH / Rey F / Zhou ZH
History
DepositionMay 21, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27057.png

Downloads & links

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Map

FileDownload / File: emd_27057.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 640 pix.
= 678.4 Å		1.06 Å/pix.
x 640 pix.
= 678.4 Å		1.06 Å/pix.
x 640 pix.
= 678.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.023259263 - 0.057836756
Average (Standard dev.)0.00027187195 (±0.0024469958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 678.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27057_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27057_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zika virus

EntireName: Zika virus
Components
  • Virus: Zika virus

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Supramolecule #1: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37499
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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