6YQ5 | pdb_00006yq5

Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - NMR Ensemble

• PDB DOI: https://doi.org/10.2210/pdb6YQ5/pdb
• BMRB: 27468
• EM Map EMD-10792: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Bacillus phage SPP1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-16 Released: 2020-10-14 
• Deposition Author(s): Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

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• Method: SOLID-STATE NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Architecture of the flexible tail tube of bacteriophage SPP1.

Zinke, M., Sachowsky, K.A.A., Oster, C., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.

(2020) Nat Commun 11: 5759-5759

• PubMed: 33188213 
• DOI: https://doi.org/10.1038/s41467-020-19611-1
• Primary Citation of Related Structures:  
  6YEG, 6YQ5


• PubMed Abstract: 
  

  Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.

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Organizational Affiliation: 

Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: scanning transmission electron microscopy

Macromolecule Content

• Total Structure Weight: 223.41 kDa 
• Atom Count: 15,756 
• Modelled Residue Count: 2,064 
• Deposited Residue Count: 2,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein gp17.1*	A, B, C, D, E, F, G, H, I, J, K, L	172	Bacillus phage SPP1	Mutation(s): 0  Gene Names: 17.1
UniProt
Find proteins for O48449 (Bacillus phage SPP1) Explore O48449  Go to UniProtKB:  O48449

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

• Method: SOLID-STATE NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: target function 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1

Structure Validation

Currently 6YQ5 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 860 TP B09
European Research Council (ERC)	Germany	337490

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-07-10
  Changes: Data collection, Database references