8ZDQ | pdb_00008zdq

Cryo-EM structure of Mycobacteriophage Douge complete baseplate (gp13, gp17, gp23, gp16, gp18 and gp20)

• PDB DOI: https://doi.org/10.2210/pdb8ZDQ/pdb
• EM Map EMD-60005: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2024-05-02 Released: 2025-06-25 
• Deposition Author(s): Maharana, J., Wang, C.H., Tsai, L.A., Lowary, T.L., Ho, M.C.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM and cryo-ET reveal the molecular architecture and host interactions of mycobacteriophage Douge.

Maharana, J., Wang, C.H., Tsai, L.A., Liao, Y.T., Yang, C.H., Shen, M.C., Macale, L.S., Tran, T.N., Narsico, J., Perez, R.J., Tewary, S.K., Wu, J.L., Lin, H.Y., Chang, S.W., Franklin, A., Moynihan, P.J., Jacobs-Sera, D., Freeman, K.G., Hatfull, G.F., Lowary, T.L., Ho, M.C.

(2025) Cell Rep 44: 116057-116057

• PubMed: 40711877 
• DOI: https://doi.org/10.1016/j.celrep.2025.116057
• Primary Citation Related Structures: 
  8ZDH, 8ZDI, 8ZDJ, 8ZDK, 8ZDL, 8ZDM, 8ZDN, 8ZDO, 8ZDP, 8ZDQ, 8ZEA


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Taiwan International Graduate Program in Chemical Biology and Molecular Biophysics (TIGP-CBMB), Academia Sinica, Taipei, Taiwan; Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Institute of Oral Medicine, National Cheng Kung University, Tainan, Taiwan.
Department of Civil Engineering, College of Engineering, National Taiwan University, Taipei, Taiwan.
Department of Civil Engineering, College of Engineering, National Taiwan University, Taipei, Taiwan; Department of Biomedical Engineering, College of Engineering, National Taiwan University, Taipei, Taiwan.
School of Biosciences, University of Birmingham, Birmingham, UK.
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 33-mer - A12B6C6D3E3F3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 33-mer - A8B6C6D4E3F3G3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,801.12 kDa 
• Atom Count: 90,393 
• Modeled Residue Count: 11,784 
• Deposited Residue Count: 16,794 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail Tube Protein (gp13)	A [auth M], B [auth N], C [auth O], D [auth P], E [auth Q], F [auth R]	300	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A5J6TI27 (Mycobacterium phage DyoEdafos) Explore A0A5J6TI27  Go to UniProtKB:  A0A5J6TI27

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tape Measure Protein (gp16)	G [auth S], H [auth T], I [auth U]	1,699	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A5J6TKG2 (Mycobacterium phage DyoEdafos) Explore A0A5J6TKG2  Go to UniProtKB:  A0A5J6TKG2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate Upper Protein (gp23)	J [auth a], K [auth b], L [auth c], M [auth d], N [auth e], O [auth f], P [auth g], Q [auth h], R [auth i], S [auth j], T [auth k], U [auth l]	311	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A5J6TI34 (Mycobacterium phage DyoEdafos) Explore A0A5J6TI34  Go to UniProtKB:  A0A5J6TI34

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Distal Tail Protein (gp17)	AA [auth r], V [auth m], W [auth n], X [auth o], Y [auth p], Z [auth q]	295	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A345MBF3 (Mycobacterium phage Bromden) Explore A0A345MBF3  Go to UniProtKB:  A0A345MBF3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate Hub Protein (gp18)	BA [auth s], CA [auth t], DA [auth u]	587	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A345MBF4 (Mycobacterium phage Bromden) Explore A0A345MBF4  Go to UniProtKB:  A0A345MBF4

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Central Fiber Protein (gp20)	EA [auth v], FA [auth w], GA [auth x]	878	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0A5J6TH08 (Mycobacterium phage DyoEdafos) Explore A0A5J6TH08  Go to UniProtKB:  A0A5J6TH08

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Maharana, J., Wang, C.H., Tsai, L.A., Lowary, T.L., Ho, M.C.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Data collection, Database references