9MFE | pdb_00009mfe

cryoEM structure of Escherichia phage YDC107 tail core

• PDB DOI: https://doi.org/10.2210/pdb9MFE/pdb
• EM Map EMD-48226: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage YDC107_1
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-01-01 
• Deposition Author(s): Kopylov, M.
• Funding Organization(s): Simons Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer

Kopylov, M., Jenkins, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 154.2 kDa 
• Atom Count: 7,110 
• Modeled Residue Count: 924 
• Deposited Residue Count: 1,470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail protein V	A, B, C, D, E, F	245	Escherichia phage YDC107_1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Kopylov, M.

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Funding Organization	Location	Grant Number
Simons Foundation	United States	SF349247

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release