8ZDM | pdb_00008zdm

Cryo-EM structure of Mycobacteriophage Douge genome-free vertex (gp8)

• PDB DOI: https://doi.org/10.2210/pdb8ZDM/pdb
• EM Map EMD-39990: EMDB EMDataResource

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


• Deposited: 2024-05-02 Released: 2025-07-16 
• 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: 4.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mycobacteriophage cryo-EM studies reveal the siphophage architecture at the amino acid level and its host interaction for viral genome ejection

Maharana, J., Wang, C.H., Tsai, L.A., Lowary, T.L., Ho, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 30-mer - A30 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,227.12 kDa 
• Atom Count: 85,025 
• Modeled Residue Count: 11,280 
• Deposited Residue Count: 11,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein (gp8)	A [auth 1], AA [auth v], B [auth 2], BA [auth w], C [auth 3], CA [auth x], D [auth 4], DA [auth y], E [auth 5], F [auth 6], G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R], M [auth m], N [auth n], O [auth o], P [auth p], Q [auth q], R [auth r], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth t], Z [auth u]	382	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
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: 2025-07-16
  Type: Initial release