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- EMDB-60001: Cryo-EM structure of Mycobacteriophage Douge Central fiber (gp20) -

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Basic information

Entry
Database: EMDB / ID: EMD-60001
TitleCryo-EM structure of Mycobacteriophage Douge Central fiber (gp20)
Map data
Sample
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Central Fiber Protein (gp20)
KeywordsMycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS / VIRAL PROTEIN
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.26 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_60001.png

Downloads & links

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Map

FileDownload / File: emd_60001.map.gz / Format: CCP4 / Size: 909.2 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 620 pix.
= 657.82 Å		1.06 Å/pix.
x 620 pix.
= 657.82 Å		1.06 Å/pix.
x 620 pix.
= 657.82 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0629506 - 1.9752105
Average (Standard dev.)-0.0013475746 (±0.03760276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions620620620
Spacing620620620
CellA=B=C: 657.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60001_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_60001_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: Central Fiber Protein (gp20)

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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: No

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Macromolecule #1: Central Fiber Protein (gp20)

MacromoleculeName: Central Fiber Protein (gp20) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 92.774414 KDa
SequenceString: MTMPNGSGGL DPGAWLSHWV NQADLSSLAG RTEDEVRAYF ENLVQADSGW GDASNTFFNL ILGGFQNLSE FVTLIVQAVT GAPGGLTDL QAFLTERWGD LADAFQAVAN LIDAIAGEVG SSLADAIAKL ATFLTELSPL NAGMLFGLIG TNHLPLLSVS H IANINPEL ...String:
MTMPNGSGGL DPGAWLSHWV NQADLSSLAG RTEDEVRAYF ENLVQADSGW GDASNTFFNL ILGGFQNLSE FVTLIVQAVT GAPGGLTDL QAFLTERWGD LADAFQAVAN LIDAIAGEVG SSLADAIAKL ATFLTELSPL NAGMLFGLIG TNHLPLLSVS H IANINPEL LVNAGFDSDV SVVDNPYWDW DGTVGRTAPL GAVKVVADGT IKDLLSGPDA IPVVEGQKLN VSAWLKYSGL VA GAGAGSI RLSGTAYSAD GEVVAYPDFG GIPDGASGTS DWTQVTGQYV VPAGVTQFRL RLSVRENATG GTVWFDDCSV KKA GLLPQG LVDGLVQALS DLLTWLESLV DNVLSALGLD PIGTIVDKIL DLADEFGDWL GATEDTAANL SNLLTKLLSD PASV IGPLA QSMITGLTGA LGNLNTAINQ IGDVLVGTVV TPINSAISNV IDWFNSLLNF QDTTTSNQIN QQNFQIATLA SGIKK QQWE CRYSTAFVTF PEMFCDWGFA LGGTTGAQST GTAHTHTLNT DGLAALQIQI LPAGYAIGGY IGISDTTIVD TIAMKM YKE TSSAINNVYL EVFREDSTGA LTSVGSVDVS GQLTTASDYV EATLPAGVIV NAGERYVVRM RNATTVGNRV GVSVMKE LV GGRELSIRTE TATDSNKTFY TPSEVLTAQG VSVIMPWAMM AAKNLATTDQ SFSDDFNRSA MGGLWFLKSD TGTNQVGV S GGRAAFSGLT DGNQNALYIR PTAGDKQWVE ATLYETGIAA SGAREGLLMH ANRDLSQVVY LGVNLNTAKI YTGPWNSLT ERASVSTTGN DVLWQMYFDP ATAAYTVLKN GQASGLTWTD SGSVVAHGPN YRFGGLRISR ATFFNAGRID NWTLKDWA

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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

MicroscopeTFS 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: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31169
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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