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- EMDB-17730: masked refinement giving rise to better defined protruding densit... -

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Basic information

Entry
Database: EMDB / ID: EMD-17730
Titlemasked refinement giving rise to better defined protruding densities of the potential macrodomain outside the AUD helical assemblies.
Map data
Sample
  • Complex: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique alphavirus domain.
    • Protein or peptide: Chikungunya virus non structural protein 3
KeywordsHelical scaffold / Replication complex / Alpha granules / Viral factories / VIRAL PROTEIN
Biological speciesChikungunya virus strain S27-African prototype
Methodhelical reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsReguera J / Hons M / Zimberger C / Ptchelkine D / Jones R / Desfosses A
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0023-01 France
ATIP-Avenir2015 France
CitationJournal: To Be Published
Title: The alphavirus nsP3 protein forms helical tubular scaffolds important for viral replication and particle assembly
Authors: Reguera J / Hons M / Zimberger C / Ptchelkine D / Jones R / Desfosses A
History
DepositionJun 25, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17730.png

Downloads & links

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Map

FileDownload / File: emd_17730.map.gz / Format: CCP4 / Size: 259.1 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 408 pix.
= 432.48 Å		1.06 Å/pix.
x 408 pix.
= 432.48 Å		1.06 Å/pix.
x 408 pix.
= 432.48 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: 0.0014
Minimum - Maximum-0.006941898 - 0.022917496
Average (Standard dev.)-0.000020683301 (±0.00083647086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 432.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Class of a mask including 16 protomers Map alligned to EMD-17729

Fileemd_17730_additional_1.map
AnnotationClass of a mask including 16 protomers Map alligned to EMD-17729
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map alligned to EMD-17729

Fileemd_17730_additional_2.map
AnnotationMap alligned to EMD-17729
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17730_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_17730_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 : Helical scaffold assembly of CHIKV nsP3 mediated by its Unique al...

EntireName: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique alphavirus domain.
Components
  • Complex: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique alphavirus domain.
    • Protein or peptide: Chikungunya virus non structural protein 3

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Supramolecule #1: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique al...

SupramoleculeName: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique alphavirus domain.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 220.25 kDa/nm

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Macromolecule #1: Chikungunya virus non structural protein 3

MacromoleculeName: Chikungunya virus non structural protein 3 / type: protein_or_peptide / ID: 1 / Details: Zn / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: APSYRVKRMD IAKNDEECVV NAANPRGLPG DGVCKAVYKK WPESFKNSAT PVGTAKTVMC GTYPVIHAVG PNFSNYSESE GDRELAAAYR EVAKEVTRLG VNSVAIPLLS TGVYSGGKDR LTQSLNHLFT AMDSTDADVV IYCRDKEWEK KISEAIQMRT QVELLDEHIS ...String:
APSYRVKRMD IAKNDEECVV NAANPRGLPG DGVCKAVYKK WPESFKNSAT PVGTAKTVMC GTYPVIHAVG PNFSNYSESE GDRELAAAYR EVAKEVTRLG VNSVAIPLLS TGVYSGGKDR LTQSLNHLFT AMDSTDADVV IYCRDKEWEK KISEAIQMRT QVELLDEHIS IDCDVVRVHP DSSLAGRKGY STTEGALYSY LEGTRFHQTA VDMAEIYTMW PKQTEANEQV CLYALGESIE SIRQKCPVDD ADASSPPKTV PCLCRYAMTP ERVTRLRMNH VTSIIVCSSF PLPKYKIEGV QKVKCSKVML FDHNVPSRVS PREYRPSQES VQEASTTTSL THSQFDLSVD GKILPVPSDL DADAPALEPA LDDGAIHTLP SATGNLAAVS DWVMSTVPVA PPRRRRGRNL TVTCDEREGN ITPMASVRFF RAELCPVVQE TAETRDTAMS LQAPPSTATE LSHPPISFGA PSETFPITFG DFNEGEIESL SSELLTFGDF LPGEVDDLTD SDWSTCSDTD DEL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
Detailshis sample was heterogeneous in lenght

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 18.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.782 Å
Applied symmetry - Helical parameters - Δ&Phi: -164.175 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 807973
Startup modelType of model: INSILICO MODEL
In silico model: Alphafold was used to have a model of the CHIKV AUD domain
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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