6YQ5

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


Experimental Data Snapshot

  • 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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Related Citations: 
    • Spinal Column Architecture of the Flexible SPP1 Bacteriophage Tail Tube
      Zinke, M., Sachowsky, K.A.A., Oster, C., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany. alange@fmp-berlin.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tail tube protein gp17.1*ABCDEFGHABCDEFGHIJKL
172Bacillus phage SPP1Mutation(s): 0 
Gene Names: 17.1
Find proteins for O48449 (Bacillus phage SPP1)
Explore O48449 
Go to UniProtKB:  O48449
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
  • OLDERADO: 6YQ5 Olderado
  • Method: SOLID-STATE NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 860 TP B09
European Research Council (ERC)Germany337490

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references