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- EMDB-0934: Sub-tomogram averaging of immature Zika virus in complex with Fab... -

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Basic information

Entry
Database: EMDB / ID: EMD-0934
TitleSub-tomogram averaging of immature Zika virus in complex with Fab DV62.5
Map data
Sample
  • Virus: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
    • Complex: Zika virus
    • Complex: anti-prM antibody DV62.5
Biological speciesZika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 / Homo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 13.0 Å
AuthorsTan TY / Fibriansah G / Kostyuchenko VA / Ng TS / Lim XX / Lim XN / Shi J / Morais MC / Corti D / Lok SM
Funding support Singapore, 3 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2012-T3-1-008 Singapore
National Research Foundation (NRF, Singapore)NRF2015NRF-CRP001-063 Singapore
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
CitationJournal: Nat Commun / Year: 2020
Title: Capsid protein structure in Zika virus reveals the flavivirus assembly process.
Authors: Ter Yong Tan / Guntur Fibriansah / Victor A Kostyuchenko / Thiam-Seng Ng / Xin-Xiang Lim / Shuijun Zhang / Xin-Ni Lim / Jiaqi Wang / Jian Shi / Marc C Morais / Davide Corti / Shee-Mei Lok /
Abstract: Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus ...Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process.
History
DepositionJan 2, 2020-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 26, 2020-
UpdateFeb 26, 2020-
Current statusFeb 26, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0934.png

Downloads & links

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Map

FileDownload / File: emd_0934.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 320 pix.
= 1094.4 Å		3.42 Å/pix.
x 320 pix.
= 1094.4 Å		3.42 Å/pix.
x 320 pix.
= 1094.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-4.5106874 - 13.627528
Average (Standard dev.)0.00000000579 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 1094.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1094.4001094.4001094.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-4.51113.6280.000

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Supplemental data

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Sample components

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Entire : Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013

EntireName: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Components
  • Virus: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
    • Complex: Zika virus
    • Complex: anti-prM antibody DV62.5

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Supramolecule #1: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013

SupramoleculeName: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: The virus was isolated from Zika patient. The immature Zika virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody DV62.5 was generated from EBV-immortalized PBMC that ...Details: The virus was isolated from Zika patient. The immature Zika virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody DV62.5 was generated from EBV-immortalized PBMC that was obtained from dengue patient.
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Supramolecule #2: Zika virus

SupramoleculeName: Zika virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #5
Source (natural)Organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Strain: H/PF/2013

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Supramolecule #3: anti-prM antibody DV62.5

SupramoleculeName: anti-prM antibody DV62.5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA, pH 8
VitrificationCryogen name: ETHANE
DetailsImmature Zika virus-Fab DV62.5 complex sample was prepared by mixing purified immature Zika virus with Fab DV62.5 at an E protein-Fab DV62.5 ratio of 1:1.1 and then the mixture was incubated at 37deg C for 30 min. The sample then was mixed with solution of 10 nm gold particles.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 47000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 1152
ExtractionNumber tomograms: 63 / Number images used: 1934 / Software - Name: emClarity
CTF correctionSoftware - Name: emClarity
Final angle assignmentType: OTHER / Software - Name: emClarity (ver. 2.1)
Details: a missing-wedge constrained cross correlation grid search

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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