9D93 | pdb_00009d93

Mycobacteriophage Bxb1 tail tip - Composite map and model

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

  • Deposited: 2024-08-20 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: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tube, gp19283Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B0A2 (Mycobacterium phage Bxb1)
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Go to UniProtKB:  Q9B0A2
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UniProt GroupQ9B0A2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tail collar spacer, gp6G [auth Ka],
H [auth Kb],
I [auth Kc]
86Mycobacterium phage Bxb1Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tail collar fibers, gp4356Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B0B7 (Mycobacterium phage Bxb1)
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UniProt GroupQ9B0B7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tip cage, gp23685Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B098 (Mycobacterium phage Bxb1)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tapemeasure proteinAA [auth Nc],
Y [auth Na],
Z [auth Nb]
823Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B099 (Mycobacterium phage Bxb1)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate hub, gp25BA [auth Oa],
CA [auth Ob],
DA [auth Oc]
600Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B096 (Mycobacterium phage Bxb1)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tail spike, gp29EA [auth Pa],
FA [auth Pb],
GA [auth Pc]
617Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B092 (Mycobacterium phage Bxb1)
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UniProt GroupQ9B092
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tail wing brush, gp33HA [auth Qa],
IA [auth Qb],
JA [auth Qc]
267Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B088 (Mycobacterium phage Bxb1)
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UniProt GroupQ9B088
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Tail wing arm, gp31106Mycobacterium phage Bxb1Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tail wing base, gp30QA [auth Sa],
RA [auth Sb],
SA [auth Sc]
496Mycobacterium phage Bxb1Mutation(s): 0 
UniProt
Find proteins for Q9B091 (Mycobacterium phage Bxb1)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 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: 2025-03-19
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-04-23
    Changes: Data collection, Database references
  • Version 1.3: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.4: 2025-06-11
    Changes: Data collection, Database references