9D9L | pdb_00009d9l

Mycobacteriophage Bxb1 tail tube segment - Composite map and model

  • Classification: VIRAL PROTEIN
  • Organism(s): Mycobacterium phage Bxb1
  • Mutation(s): No 

  • Deposited: 2024-08-21 Released: 2024-09-25 
  • Deposition Author(s): Freeman, K.G.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), National Institutes of Health/Office of the Director, Academia Sinica (Taiwan)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and infection dynamics of mycobacteriophage Bxb1.

Freeman, K.G.Mondal, S.Macale, L.S.Podgorski, J.White, S.J.Silva, B.H.Ortiz, V.Huet, A.Perez, R.J.Narsico, J.T.Ho, M.C.Jacobs-Sera, D.Lowary, T.L.Conway, J.F.Park, D.Hatfull, G.F.

(2025) Cell 188: 2925

  • DOI: https://doi.org/10.1016/j.cell.2025.03.027
  • Primary Citation of Related Structures:  
    9D93, 9D94, 9D9L, 9D9W, 9D9X

  • PubMed Abstract: 

    Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages show considerable potential as therapies for Mycobacterium infections, but little is known about the structural details of these phages or how they bind to and traverse the complex Mycobacterium cell wall. Here, we report the complete structure and atomic model of phage Bxb1, including the arrangement of immunodominant domains of both the capsid and tail tube subunits, as well as the assembly of the protein subunits in the tail-tip complex. The structure contains protein assemblies with 3-, 5-, 6-, and 12-fold symmetries, which interact to satisfy several symmetry mismatches. Cryoelectron tomography of phage particles bound to M. smegmatis reveals the structural transitions that occur for free phage particles to bind to the cell surface and navigate through the cell wall to enable DNA transfer into the cytoplasm.


  • Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major tail protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
283Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B0A2 (Mycobacterium phage Bxb1)
Explore Q9B0A2 
Go to UniProtKB:  Q9B0A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B0A2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesK99AI173544
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116884
Howard Hughes Medical Institute (HHMI)United StatesGT12053
National Institutes of Health/Office of the DirectorUnited StatesS10 OD025009
National Institutes of Health/Office of the DirectorUnited StatesS10 OD019995
National Institutes of Health/Office of the DirectorUnited StatesS10OD032467
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547
Academia Sinica (Taiwan)TaiwanAS-IDR-110-06

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-11
    Changes: Data collection, Database references