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- EMDB-61002: VLP structure of Chikungunya virus complexed with C34 Fab, 3f block -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-61002
TitleVLP structure of Chikungunya virus complexed with C34 Fab, 3f block
Map data
Sample
  • Complex: CHIKV VLP
Keywordschikungunya / alphavirus / VIRUS LIKE PARTICLE / antibody
Biological speciesChikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsHan X / Ji C / Wang F / Tian S / Gao FG / Yan J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: VLP structure of Chikungunya virus complexed with C34 Fab, 2f block.
Authors: Han X / Ji C / Wang F / Tian S / Gao FG / Yan J
History
DepositionJul 31, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61002.png

Downloads & links

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Map

FileDownload / File: emd_61002.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 290 pix.
= 388.6 Å		1.34 Å/pix.
x 290 pix.
= 388.6 Å		1.34 Å/pix.
x 290 pix.
= 388.6 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: 0.145
Minimum - Maximum-0.7196403 - 1.1420532
Average (Standard dev.)0.0032270246 (±0.04789966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 388.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61002_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_61002_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 : CHIKV VLP

EntireName: CHIKV VLP
Components
  • Complex: CHIKV VLP

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Supramolecule #1: CHIKV VLP

SupramoleculeName: CHIKV VLP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chikungunya 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

BufferpH: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fcg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 531640
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial model
PDB IDChain

8fcg

source_name: PDB, initial_model_type: experimental model

6jo8

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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