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- EMDB-39989: Cryo-EM structure of Mycobacteriophage Douge genome-free connecto... -

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Basic information

Entry
Database: EMDB / ID: EMD-39989
TitleCryo-EM structure of Mycobacteriophage Douge genome-free connector (gp5, gp9, gp10, gp12 and gp13)
Map data
Sample
  • Virus: Mycolicibacterium smegmatis MC2 155 (bacteria)
    • Protein or peptide: Protal Protein (gp5)
    • Protein or peptide: Adaptor Protein (gp9)
    • Protein or peptide: Stopper Protein (gp10)
    • Protein or peptide: Terminator Protein (gp12)
    • Protein or peptide: Tail Tube Protein (gp13)
KeywordsMycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS / VIRAL PROTEIN
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 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_39989.png

Downloads & links

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Map

FileDownload / File: emd_39989.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.43101525 - 0.99968773
Average (Standard dev.)0.001810847 (±0.04459014)
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: #1

Fileemd_39989_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_39989_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: Protal Protein (gp5)
    • Protein or peptide: Adaptor Protein (gp9)
    • Protein or peptide: Stopper Protein (gp10)
    • Protein or peptide: Terminator Protein (gp12)
    • Protein or peptide: Tail Tube Protein (gp13)

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Supramolecule #1: Mycolicibacterium smegmatis MC2 155

SupramoleculeName: Mycolicibacterium smegmatis MC2 155 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1, #4, #2, #5, #3 / 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: Protal Protein (gp5)

MacromoleculeName: Protal Protein (gp5) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 60.435762 KDa
SequenceString: MIELPDAISD GEVRKLVENE FWPEFVRRRE KLDRIAQWAR GEQPDYLIQN ANREKRALLK LAKTPWLGLV VTHFTQALFV DGYRAEGSK ENAKGPWQTW NANKMQSKQI AIHRAALTYG YSYARVLPGV ALDGANQAEI HGVSPRRLLA LYEDQINDEY P KYALELAN ...String:
MIELPDAISD GEVRKLVENE FWPEFVRRRE KLDRIAQWAR GEQPDYLIQN ANREKRALLK LAKTPWLGLV VTHFTQALFV DGYRAEGSK ENAKGPWQTW NANKMQSKQI AIHRAALTYG YSYARVLPGV ALDGANQAEI HGVSPRRLLA LYEDQINDEY P KYALELAN NGKTVRLYTD TDYYELRMPS PGNFPNEQVI KKVHHGVGVC PFVRYVNMMD LDGFTMGEVE YLVPVASKID KT DYDRLLA QHYNSWKVKV ATGIDDLSED ATPEEQQRAK LILAQDDILM HGNHEAKFYT LPETSLDGFI AAHTQDVEIL ANN AQVPVW ILNGQLANLS ADALTAATKG TIQKLYERQV TFGAAHNQVL RLAAHVEGDT EGARDFTASV SWQDTSVRSL AQAV DAYGK AATMLGMPKE FLWGLIPGIT KTDVEAMRQH FNDDDEMTQM LLWWTPNGPG GEFAAEIEVD SQTQIIEAQG DVQKD LQDA QAKAQADLAK QNAAAQQRQA VAVAKATPAA SKAPSTSKAA SKRTPKKQGG VSGNDPASRA A

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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: 12.405641 KDa
SequenceString:
MNDETLTVYR GATDNKGNPN KQVHGTVKGV FAWGPGTSTN KFGRDRNFKG ESSSLTAELY VKRGADLKAR DRIRRANGEE YSVVGHAAW DQGHPFDGFD FGYMVFQVEA VNA

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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: 32.112025 KDa
SequenceString: MTDFYTIKDA QADLAIAPLN LTVLLAPYST TPATTLESPT DGSLAIPPGY KSVGHFEKQA GLTLGNEFDS KDIEAYGEPE PIRTIINKR TTTFDFAMYQ NQRNVLELIW TQDFSNIQPS EFGGIVLEAP KVPKNIYYRA ILVGMDDRND RPIWLYWLMP K VKLDKLDN ...String:
MTDFYTIKDA QADLAIAPLN LTVLLAPYST TPATTLESPT DGSLAIPPGY KSVGHFEKQA GLTLGNEFDS KDIEAYGEPE PIRTIINKR TTTFDFAMYQ NQRNVLELIW TQDFSNIQPS EFGGIVLEAP KVPKNIYYRA ILVGMDDRND RPIWLYWLMP K VKLDKLDN QTLNDDNVIE YKPTLKAFRD DVVGYSVAQG FAGPGWRDLV ATAGFGEALT ALTITPGSPT VTVATGASHT AQ LLVEGDN GINYTPDVVF TSSAPDKASV SAAGLVTGVA AGSATITATK GALTATATVT VTA

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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: 17.134275 KDa
SequenceString:
MAGLATIDEL QTLMSTVFED DALEQAQLVL DIVSSWARVV SGQMWPDAPA NVPDDVRAVV LQASRRELKN PDRVISRQMG PFNVQYSQP PDGFFYPAEL AILKRFKRSG GLMTVSTSRG EEGRPWAGKT AYIRYGDGLF PFCSEDEGYG DVVPW

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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: 19.22099 KDa
SequenceString:
MAVVLPDWYE EAFVNVENLF IDMFTDLLPD YESGCWAPDD WLADEIEVKP TIWFFRLPGG RVDWDGRKDE CQLQVMVVTG SRDDSWRLM DFVRAMLLPM QGDKYKMADG YTAQIRCAGE VAGPQLLTPG QRIDTRVVTA TFKVSVSMKS AKNYKQKLYE L WQALRGS

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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: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3700
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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