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- EMDB-39978: Cryo-EM structure of Mycobacteriophage Douge genome-free capsid (gp8) -

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Basic information

Entry
Database: EMDB / ID: EMD-39978
TitleCryo-EM structure of Mycobacteriophage Douge genome-free capsid (gp8)
Map data
Sample
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Major Capsid Protein (gp8)
KeywordsMycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsMaharana J / Wang CH / Tsai LA / Lowary TL / Ho MC
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Mycobacteriophage cryo-EM studies reveal the siphophage architecture at the amino acid level and its host interaction for viral genome ejection
Authors: Maharana J / Wang CH / Tsai LA / Lowary TL / Ho MC
History
DepositionMay 2, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39978.png

Downloads & links

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Map

FileDownload / File: emd_39978.map.gz / Format: CCP4 / Size: 2.4 GB / 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 860 pix.
= 912.46 Å		1.06 Å/pix.
x 860 pix.
= 912.46 Å		1.06 Å/pix.
x 860 pix.
= 912.46 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.57505196 - 1.6378915
Average (Standard dev.)0.0069431984 (±0.10080431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-429-429-429
Dimensions860860860
Spacing860860860
CellA=B=C: 912.45996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39978_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_39978_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 : Mycolicibacterium smegmatis MC2 155

EntireName: Mycolicibacterium smegmatis MC2 155 (bacteria)
Components
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Major Capsid Protein (gp8)

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Supramolecule #1: Mycolicibacterium smegmatis MC2 155

SupramoleculeName: Mycolicibacterium smegmatis MC2 155 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 246196 / Sci species name: Mycolicibacterium smegmatis MC2 155 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major Capsid Protein (gp8)

MacromoleculeName: Major Capsid Protein (gp8) / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 40.904098 KDa
SequenceString: MAHIFVKPEL VAEIGVKQLQ REIVLPGLVW TNPLTDFGGS KNDTITVRVP AITTANRRDL RDPDRTVIAS ELVEHSFGVT LDKHVYAAL KFTDEQRTLD IRDYTKQVLM PQVSAVAYEL EDYIAELIEG APYEETILID PADTVPAFIT ADQRMGEANV P TDSRRLVV ...String:
MAHIFVKPEL VAEIGVKQLQ REIVLPGLVW TNPLTDFGGS KNDTITVRVP AITTANRRDL RDPDRTVIAS ELVEHSFGVT LDKHVYAAL KFTDEQRTLD IRDYTKQVLM PQVSAVAYEL EDYIAELIEG APYEETILID PADTVPAFIT ADQRMGEANV P TDSRRLVV GSAVAAALAK DKQFRHADWS GDQANAALRE AHVGRLAGMN VIRSNAIAPD KAYLWHRTAF ILAYRTPVVP EG AKAGASF SANGVALRWL ADYDYSQLGD RTLLDVFTGR KVVTEVDGSF VRAVELQLQA SSITIVGGAF ALATTTGTKQ LKV RDDNGT DVTARCTFAS SAGTKATVSA AGLVTGVAAG TADITASYVP PQGGTAKTAT VTVTVP

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 3.0 µm / Nominal defocus min: 0.43 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21074
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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