7KH1 | pdb_00007kh1

Baseplate Complex for Myoviridae Phage XM1

• PDB DOI: https://doi.org/10.2210/pdb7KH1/pdb
• EM Map EMD-22873: EMDB EMDataResource

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


• Deposited: 2020-10-19 Released: 2021-10-27 
• 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: 3.20 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 48-mer - A12B6C6D6E6F6G6 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Hetero 48-mer - A6B6C6D6E6F6G6H6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 1,434.35 kDa 
• Atom Count: 97,344 
• Modeled Residue Count: 12,588 
• Deposited Residue Count: 13,050 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tail tube protein, gp7	A [auth A1], B [auth B1], C [auth C1], D [auth D1], E [auth E1], F [auth F1]	143	Vibrio phage XM1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
baseplate wedge protein, gp17	G [auth A2], H [auth B2], I [auth C2], J [auth D2], K [auth E2], L [auth F2]	242	Vibrio phage XM1	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
baseplate organization protein, gp11	M [auth A3], N [auth B3], O [auth C3], P [auth D3], Q [auth E3], R [auth F3]	250	Vibrio phage XM1	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
baseplate stabilizing protein, gp12	S [auth A4], T [auth B4], U [auth C4], V [auth D4], W [auth E4], X [auth F4]	118	Vibrio phage XM1	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
baseplate wedge protein, gp16	AA [auth C5], BA [auth D5], CA [auth E5], DA [auth F5], EA [auth G5], FA [auth H5], GA [auth I5], HA [auth J5], IA [auth K5], JA [auth L5], Y [auth A5], Z [auth B5]	404	Vibrio phage XM1	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
tail sheath protein, gp6	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

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
tail sheath initiator protein, gp15	QA [auth A7], RA [auth B7], SA [auth C7], TA [auth D7], UA [auth E7], VA [auth F7]	117	Vibrio phage XM1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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: 2021-10-27 
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: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection, Database references