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- EMDB-52385: Localized reconstruction consensus map of minor protein P7 from t... -

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Basic information

Entry
Database: EMDB / ID: EMD-52385
TitleLocalized reconstruction consensus map of minor protein P7 from transcribing particles of bacteriophage phi6
Map data
Sample
  • Virus: Cystovirus phi6
    • Protein or peptide: Nucleocapsid protein
Keywordscystovirus / phi6 / semi-conservative transcription / cryo-EM / cryogenic electron microscopy / localized reconstruction / symmetry relaxation / virus / dsRNA virus / bacteriophage
Function / homologyviral nucleocapsid / Nucleocapsid protein
Function and homology information
Biological speciesCystovirus phi6
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsIlca SL / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Academy of Finland331627 Finland
CitationJournal: To Be Published
Title: Restructuring of bacteriophage phi6 viral particle activates semi-conservative transcription
Authors: Ilca SL / Sun X / Kumpula E-P / Eskelin K / Poranen MM / Huiskonen JT
History
DepositionDec 20, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52385.png

Downloads & links

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Map

FileDownload / File: emd_52385.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 232 pix.
= 324.8 Å		1.4 Å/pix.
x 232 pix.
= 324.8 Å		1.4 Å/pix.
x 232 pix.
= 324.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.09151266 - 0.16885284
Average (Standard dev.)0.00020240319 (±0.0146291675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions232232232
Spacing232232232
CellA=B=C: 324.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52385_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52385_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52385_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 : Cystovirus phi6

EntireName: Cystovirus phi6
Components
  • Virus: Cystovirus phi6
    • Protein or peptide: Nucleocapsid protein

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Supramolecule #1: Cystovirus phi6

SupramoleculeName: Cystovirus phi6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10879 / Sci species name: Cystovirus phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: Outer protein shell / T number (triangulation number): 13
Virus shellShell ID: 2 / Name: Inner protein shell / T number (triangulation number): 1

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Macromolecule #1: Nucleocapsid protein

MacromoleculeName: Nucleocapsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cystovirus phi6
Molecular weightTheoretical: 12.017965 KDa
SequenceString:
TLYLVPPLDS ADKELPALAS KAGVTLLEIE FLHELWPHLS GGQIVIAALN ANNLAILNRH MSTLLVELPV AVMAVPGASY RSDWNMIAH ALPSEDWITL SNKMLKSGLL AN

UniProtKB: Nucleocapsid protein

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 41.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

0299

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114297
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9htw:
Minor protein P7 dimer from transcribing particles of bacteriophage phi6

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