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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: Cell Rep / Year: 2025
Title: Cryo-EM and cryo-ET reveal the molecular architecture and host interactions of mycobacteriophage Douge.
Authors: Jitendra Maharana / Chun-Hsiung Wang / Li-An Tsai / Yi-Ting Liao / Cheng-Han Yang / Melvin C Shen / Lourriel S Macale / Thang Ngoc Tran / Joemark Narsico / Ronelito J Perez / Sunil Kumar ...Authors: Jitendra Maharana / Chun-Hsiung Wang / Li-An Tsai / Yi-Ting Liao / Cheng-Han Yang / Melvin C Shen / Lourriel S Macale / Thang Ngoc Tran / Joemark Narsico / Ronelito J Perez / Sunil Kumar Tewary / Jian-Li Wu / Hong-You Lin / Shu-Wei Chang / Aaron Franklin / Patrick J Moynihan / Deborah Jacobs-Sera / Krista G Freeman / Graham F Hatfull / Todd L Lowary / Meng-Chiao Ho /
Abstract: Recent reports highlight the efficacy of engineered mycobacteriophages to treat non-tuberculosis mycobacterial disease. Molecular insights into mycobacteriophage architecture and host interactions ...Recent reports highlight the efficacy of engineered mycobacteriophages to treat non-tuberculosis mycobacterial disease. Molecular insights into mycobacteriophage architecture and host interactions could allow structure-guided phage engineering to increase efficacy and broaden host range, but such information is currently unavailable. We describe the cryoelectron microscopy (cryo-EM) structure of mycobacteriophage Douge, which contains 1,105 protein subunits assembled into a complete siphophage and is coated with glycan-binding domains for mycobacterial cell surface interactions. When filled with viral genome, the channel spanning the connector, tail, and baseplate is sealed by tape measure proteins, providing a genome gating system and requiring limited structural changes for genome ejection upon phage-host contact. Nanometer-resolution cryoelectron tomography (cryo-ET) snapshots of phage-host interactions show that the baseplate remains attached to the mycobacterial outer membrane during viral genome ejection. This study reveals high-resolution structural details of this mycobacteriophage and its interaction with host glycans.
History
DepositionMay 2, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 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
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
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
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Half map: #1

Fileemd_60001_half_map_2.map
Projections & Slices
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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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