7KLN | pdb_00007kln

Myoviridae Phage XM1 Neck Region (12-fold)

• PDB DOI: https://doi.org/10.2210/pdb7KLN/pdb
• EM Map EMD-22917: EMDB EMDataResource

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


• Deposited: 2020-10-30 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 - C12  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 717.19 kDa 
• Atom Count: 45,564 
• Modeled Residue Count: 5,748 
• Deposited Residue Count: 6,360 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A [auth A1], B [auth B1], C [auth C1], D [auth D1], E [auth E1], F [auth F1], G [auth G1], H [auth H1], I [auth I1], J [auth J1], K [auth K1], L [auth L1]	412	Vibrio phage XM1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Head completion protein, gp1	M [auth A2], N [auth B2], O [auth C2], P [auth D2], Q [auth E2], R [auth F2], S [auth G2], T [auth H2], U [auth I2], V [auth J2], W [auth K2], X [auth L2]	118	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 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	jspr

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: 2024-11-06
  Changes: Data collection, Database references, Structure summary