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- EMDB-39983: Cryo-EM structure of Mycobacteriophage Douge genome-packed connec... -

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Basic information

Entry
Database: EMDB / ID: EMD-39983
TitleCryo-EM structure of Mycobacteriophage Douge genome-packed connector (gp5, gp9, gp10, gp12 and gp13)
Map data
Sample
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Portal Protein (gp5)
    • Protein or peptide: Stopper Protein (gp10)
    • Protein or peptide: Tail Tube Protein (gp13)
    • Protein or peptide: Adaptor Protein (gp9)
    • Protein or peptide: Terminator Protein (gp12)
KeywordsMycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS / VIRAL PROTEIN
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 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_39983.png

Downloads & links

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Map

FileDownload / File: emd_39983.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å

Surface

Projections

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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-0.7433553 - 1.1568037
Average (Standard dev.)-0.0027606671 (±0.039421253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 543.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39983_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_39983_half_map_2.map
Projections & Slices
AxesZYX

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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: Portal Protein (gp5)
    • Protein or peptide: Stopper Protein (gp10)
    • Protein or peptide: Tail Tube Protein (gp13)
    • Protein or peptide: Adaptor Protein (gp9)
    • Protein or peptide: Terminator Protein (gp12)

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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: Portal Protein (gp5)

MacromoleculeName: Portal Protein (gp5) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 56.662449 KDa
SequenceString: IELPDAISDG EVRKLVENEF WPEFVRRREK LDRIAQWARG EQPDYLIQNA NREKRALLKL AKTPWLGLVV THFTQALFVD GYRAEGSKE NAKGPWQTWN ANKMQSKQIA IHRAALTYGY SYARVLPGVA LDGANQAEIH GVSPRRLLAL YEDQINDEYP K YALELANN ...String:
IELPDAISDG EVRKLVENEF WPEFVRRREK LDRIAQWARG EQPDYLIQNA NREKRALLKL AKTPWLGLVV THFTQALFVD GYRAEGSKE NAKGPWQTWN ANKMQSKQIA IHRAALTYGY SYARVLPGVA LDGANQAEIH GVSPRRLLAL YEDQINDEYP K YALELANN GKTVRLYTDT DYYELRMPSP GNFPNEQVIK KVHHGVGVCP FVRYVNMMDL DGFTMGEVEY LVPVASKIDK TD YDRLLAQ HYNSWKVKVA TGIDDLSEDA TPEEQQRAKL ILAQDDILMH GNHEAKFYTL PETSLDGFIA AHTQDVEILA NNA QVPVWI LNGQLANLSA DALTAATKGT IQKLYERQVT FGAAHNQVLR LAAHVEGDTE GARDFTASVS WQDTSVRSLA QAVD AYGKA ATMLGMPKEF LWGLIPGITK TDVEAMRQHF NDDDEMTQML LWWTPNGPGG EFAAEIEVDS QTQIIEAQGD VQKDL QDAQ AKAQADLAKQ NAAAQQRQAV AV

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Macromolecule #2: Stopper Protein (gp10)

MacromoleculeName: Stopper Protein (gp10) / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 12.334563 KDa
SequenceString:
MNDETLTVYR GATDNKGNPN KQVHGTVKGV FAWGPGTSTN KFGRDRNFKG ESSSLTAELY VKRGADLKAR DRIRRANGEE YSVVGHAAW DQGHPFDGFD FGYMVFQVEA VN

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Macromolecule #3: Tail Tube Protein (gp13)

MacromoleculeName: Tail Tube Protein (gp13) / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 31.98083 KDa
SequenceString: TDFYTIKDAQ ADLAIAPLNL TVLLAPYSTT PATTLESPTD GSLAIPPGYK SVGHFEKQAG LTLGNEFDSK DIEAYGEPEP IRTIINKRT TTFDFAMYQN QRNVLELIWT QDFSNIQPSE FGGIVLEAPK VPKNIYYRAI LVGMDDRNDR PIWLYWLMPK V KLDKLDNQ ...String:
TDFYTIKDAQ ADLAIAPLNL TVLLAPYSTT PATTLESPTD GSLAIPPGYK SVGHFEKQAG LTLGNEFDSK DIEAYGEPEP IRTIINKRT TTFDFAMYQN QRNVLELIWT QDFSNIQPSE FGGIVLEAPK VPKNIYYRAI LVGMDDRNDR PIWLYWLMPK V KLDKLDNQ TLNDDNVIEY KPTLKAFRDD VVGYSVAQGF AGPGWRDLVA TAGFGEALTA LTITPGSPTV TVATGASHTA QL LVEGDNG INYTPDVVFT SSAPDKASVS AAGLVTGVAA GSATITATKG ALTATATVTV TA

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Macromolecule #4: Adaptor Protein (gp9)

MacromoleculeName: Adaptor Protein (gp9) / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 15.174126 KDa
SequenceString:
AGLATIDELQ TLMSTVFEDD ALEQAQLVLD IVSSWARVVS GQMWPDAPAN VPDDVRAVVL QASRRELKNP DRVISRQMGP FNVQYSQPP DGFFYPAELA ILKRFKRSGG LMTVSTSRGE EGRPWAGKTA YIRYGDGL

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Macromolecule #5: Terminator Protein (gp12)

MacromoleculeName: Terminator Protein (gp12) / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 19.002715 KDa
SequenceString:
AVVLPDWYEE AFVNVENLFI DMFTDLLPDY ESGCWAPDDW LADEIEVKPT IWFFRLPGGR VDWDGRKDEC QLQVMVVTGS RDDSWRLMD FVRAMLLPMQ GDKYKMADGY TAQIRCAGEV AGPQLLTPGQ RIDTRVVTAT FKVSVSMKSA KNYKQKLYEL W QALRG

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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: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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