7KJK | pdb_00007kjk

The Neck region of Phage XM1 (6-fold symmetry)

• PDB DOI: https://doi.org/10.2210/pdb7KJK/pdb
• EM Map EMD-22896: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Vibrio phage XM1
• Mutation(s): No 


• Deposited: 2020-10-26 Released: 2021-11-03 
• Deposition Author(s): Wang, Z., Klose, T., Jiang, W., Kuhn, R.J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Vibrio phage XM1, a simple contractile DNA injection machine

Wang, Z., Fokine, A., Guo, X., Jiang, W., Rossmann, M.G., Kuhn, R.J., Luo, Z.H., Klose, T.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.12.18.469577

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 42-mer - A18B6C6D6E6 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Hetero 42-mer - A12B6C6D6E6F6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 2,232.19 kDa 
• Atom Count: 59,088 
• Modeled Residue Count: 7,740 
• Deposited Residue Count: 20,592 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail terminator protein	A [auth A5], B [auth B5], C [auth C5], D [auth D5], E [auth E5], F [auth F5]	161	Vibrio phage XM1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collar spike protein	G [auth A3], H [auth B3], I [auth C3], J [auth D3], K [auth E3], L [auth F3], M [auth G3], N [auth H3], O [auth I3], P [auth J3], Q [auth K3], R [auth L3], S [auth M3], T [auth N3], U [auth O3], V [auth P3], W [auth Q3], X [auth R3]	839	Vibrio phage XM1	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Head completion protein	AA [auth C4], BA [auth D4], CA [auth E4], DA [auth F4], Y [auth A4], Z [auth B4]	114	Vibrio phage XM1	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein	EA [auth A7], FA [auth B7], GA [auth C7], HA [auth D7], IA [auth E7], JA [auth F7]	143	Vibrio phage XM1	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail sheath protein	KA [auth A6], LA [auth B6], MA [auth C6], NA [auth D6], OA [auth E6], PA [auth F6]	497	Vibrio phage XM1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Wang, Z., Klose, T., Jiang, W., Kuhn, R.J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection, Database references