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- PDB-8zdm: Cryo-EM structure of Mycobacteriophage Douge genome-free vertex (gp8) -

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Basic information

Entry
Database: PDB / ID: 8zdm
TitleCryo-EM structure of Mycobacteriophage Douge genome-free vertex (gp8)
ComponentsMajor capsid protein (gp8)
KeywordsVIRAL PROTEIN / Mycobacteriophage / phage structure / Icosahedral / cryo-EM / protein assembly / VIRUS
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsMaharana, J. / Wang, C.H. / Tsai, L.A. / Lowary, T.L. / Ho, M.C.
Funding support Taiwan, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Major capsid protein (gp8)
2: Major capsid protein (gp8)
3: Major capsid protein (gp8)
4: Major capsid protein (gp8)
5: Major capsid protein (gp8)
6: Major capsid protein (gp8)
M: Major capsid protein (gp8)
N: Major capsid protein (gp8)
O: Major capsid protein (gp8)
P: Major capsid protein (gp8)
Q: Major capsid protein (gp8)
R: Major capsid protein (gp8)
m: Major capsid protein (gp8)
n: Major capsid protein (gp8)
o: Major capsid protein (gp8)
p: Major capsid protein (gp8)
q: Major capsid protein (gp8)
r: Major capsid protein (gp8)
T: Major capsid protein (gp8)
U: Major capsid protein (gp8)
V: Major capsid protein (gp8)
W: Major capsid protein (gp8)
X: Major capsid protein (gp8)
Y: Major capsid protein (gp8)
t: Major capsid protein (gp8)
u: Major capsid protein (gp8)
v: Major capsid protein (gp8)
w: Major capsid protein (gp8)
x: Major capsid protein (gp8)
y: Major capsid protein (gp8)


Theoretical massNumber of molelcules
Total (without water)1,227,12330
Polymers1,227,12330
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Major capsid protein (gp8)


Mass: 40904.098 Da / Num. of mol.: 30 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycolicibacterium smegmatis MC2 155 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 430 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3700 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00286505
ELECTRON MICROSCOPYf_angle_d0.505118050
ELECTRON MICROSCOPYf_dihedral_angle_d13.05230850
ELECTRON MICROSCOPYf_chiral_restr0.04314235
ELECTRON MICROSCOPYf_plane_restr0.00315290

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