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- PDB-8zdo: Cryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp1... -

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Basic information

Entry
Database: PDB / ID: 8zdo
TitleCryo-EM structure of Mycobacteriophage Douge baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)
Components
  • Baseplate hub protein (gp18)
  • Baseplate upper protein (gp23)
  • Central fiber protein (gp20)
  • Distal tail protein (gp17)
  • Tail tube protein (gp13)
  • Tape measure protein (gp16)
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: 2.97 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 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Tail tube protein (gp13)
H: Tail tube protein (gp13)
I: Tail tube protein (gp13)
J: Tail tube protein (gp13)
K: Tail tube protein (gp13)
L: Tail tube protein (gp13)
M: Tail tube protein (gp13)
N: Tail tube protein (gp13)
O: Tail tube protein (gp13)
P: Tail tube protein (gp13)
Q: Tail tube protein (gp13)
R: Tail tube protein (gp13)
S: Tape measure protein (gp16)
T: Tape measure protein (gp16)
U: Tape measure protein (gp16)
a: Baseplate upper protein (gp23)
b: Baseplate upper protein (gp23)
c: Baseplate upper protein (gp23)
d: Baseplate upper protein (gp23)
e: Baseplate upper protein (gp23)
f: Baseplate upper protein (gp23)
g: Baseplate upper protein (gp23)
h: Baseplate upper protein (gp23)
i: Baseplate upper protein (gp23)
j: Baseplate upper protein (gp23)
k: Baseplate upper protein (gp23)
l: Baseplate upper protein (gp23)
m: Distal tail protein (gp17)
n: Distal tail protein (gp17)
o: Distal tail protein (gp17)
p: Distal tail protein (gp17)
q: Distal tail protein (gp17)
r: Distal tail protein (gp17)
s: Baseplate hub protein (gp18)
t: Baseplate hub protein (gp18)
u: Baseplate hub protein (gp18)
v: Central fiber protein (gp20)
w: Central fiber protein (gp20)
x: Central fiber protein (gp20)


Theoretical massNumber of molelcules
Total (without water)1,993,79239
Polymers1,993,79239
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

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Protein , 6 types, 39 molecules GHIJKLMNOPQRSTUabcdefghijklmno...

#1: Protein
Tail tube protein (gp13)


Mass: 32112.025 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#2: Protein Tape measure protein (gp16)


Mass: 176109.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#3: Protein
Baseplate upper protein (gp23)


Mass: 33673.859 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#4: Protein
Distal tail protein (gp17)


Mass: 33771.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#5: Protein Baseplate hub protein (gp18)


Mass: 65026.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#6: Protein Central fiber protein (gp20)


Mass: 92774.414 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)

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Details

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: FEI TITAN 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78927 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00489196
ELECTRON MICROSCOPYf_angle_d0.527121953
ELECTRON MICROSCOPYf_dihedral_angle_d12.51831548
ELECTRON MICROSCOPYf_chiral_restr0.04413644
ELECTRON MICROSCOPYf_plane_restr0.00415768

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