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- EMDB-15898: Recombinant Mayaro virus-like particle -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15898
TitleRecombinant Mayaro virus-like particle
Map dataMain map
Sample
  • Complex: Virus-like particle of Mayaro virus
KeywordsMayaro virus / MAYV / vaccine candidate / immunogen / VIRUS LIKE PARTICLE
Biological speciesMayaro virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKim YC / Song X / Huiskonen JT
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust2241117/Z/21/Z United Kingdom
CitationJournal: To Be Published
Title: Immunogenic recombinant Mayaro Virus-Like Particles present natively assembled glycoprotein
Authors: Kim YC / Watanabe Y / Arlen-Celina L / Song X / Stass R / Azar SR / Rossi SL / Kuemmerer BM / Crispin M / Bowden TA / Huiskonen JT / Reyes-Sandoval A
History
DepositionSep 28, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15898.png

Downloads & links

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Map

FileDownload / File: emd_15898.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02455204 - 0.032231644
Average (Standard dev.)0.00018899709 (±0.0021467179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1072.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap 2

Fileemd_15898_half_map_1.map
AnnotationHalfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 1

Fileemd_15898_half_map_2.map
AnnotationHalfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Virus-like particle of Mayaro virus

EntireName: Virus-like particle of Mayaro virus
Components
  • Complex: Virus-like particle of Mayaro virus

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Supramolecule #1: Virus-like particle of Mayaro virus

SupramoleculeName: Virus-like particle of Mayaro virus / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mayaro virus

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 32989
Startup modelType of model: OTHER / Details: Ab initio in RELION
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 50 / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 26857
FSC plot (resolution estimation)

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