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- PDB-9d93: Mycobacteriophage Bxb1 tail tip - Composite map and model -

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Basic information

Entry
Database: PDB / ID: 9d93
TitleMycobacteriophage Bxb1 tail tip - Composite map and model
Components
  • Baseplate hub, gp25
  • Tail collar fibers, gp4
  • Tail collar spacer, gp6
  • Tail spike, gp29
  • Tail tip cage, gp23
  • Tail tube, gp19
  • Tail wing arm, gp31
  • Tail wing base, gp30
  • Tail wing brush, gp33
  • Tapemeasure protein
KeywordsVIRAL PROTEIN / Bacteriophage / tail tip
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Fibronectin type III / Beta-lactamase/transpeptidase-like / Immunoglobulin-like fold
Similarity search - Domain/homology
Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Tapemeasure protein / Major tail protein / Minor tail protein
Similarity search - Component
Biological speciesMycobacterium phage Bxb1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsFreeman, K.G.
Funding support United States, Taiwan, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI173544 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116884 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorS10 OD025009 United States
National Institutes of Health/Office of the DirectorS10 OD019995 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
Academia Sinica (Taiwan)AS-IDR-110-06 Taiwan
CitationJournal: Cell / Year: 2025
Title: Structure and infection dynamics of mycobacteriophage Bxb1.
Authors: Krista G Freeman / Sudipta Mondal / Lourriel S Macale / Jennifer Podgorski / Simon J White / Benjamin H Silva / Valery Ortiz / Alexis Huet / Ronelito J Perez / Joemark T Narsico / Meng-Chiao ...Authors: Krista G Freeman / Sudipta Mondal / Lourriel S Macale / Jennifer Podgorski / Simon J White / Benjamin H Silva / Valery Ortiz / Alexis Huet / Ronelito J Perez / Joemark T Narsico / Meng-Chiao Ho / Deborah Jacobs-Sera / Todd L Lowary / James F Conway / Donghyun Park / Graham F Hatfull /
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 ...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.
History
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Structure summary
Category: em_admin / entity ...em_admin / entity / pdbx_entry_details / pdbx_related_exp_data_set
Item: _em_admin.last_update / _entity.pdbx_description
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Structure summary / Data content type: EM metadata / EM metadata / Category: em_admin / entity / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _entity.pdbx_description
Revision 1.2Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update
Revision 1.3Apr 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.4Jun 11, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ja: Tail tube, gp19
Jb: Tail tube, gp19
Jc: Tail tube, gp19
Jd: Tail tube, gp19
Je: Tail tube, gp19
Jf: Tail tube, gp19
Ka: Tail collar spacer, gp6
Kb: Tail collar spacer, gp6
Kc: Tail collar spacer, gp6
La: Tail collar fibers, gp4
Lb: Tail collar fibers, gp4
Lc: Tail collar fibers, gp4
Ld: Tail collar fibers, gp4
Le: Tail collar fibers, gp4
Lf: Tail collar fibers, gp4
Lg: Tail collar fibers, gp4
Lh: Tail collar fibers, gp4
Li: Tail collar fibers, gp4
Ma: Tail tip cage, gp23
Mb: Tail tip cage, gp23
Mc: Tail tip cage, gp23
Md: Tail tip cage, gp23
Me: Tail tip cage, gp23
Mf: Tail tip cage, gp23
Na: Tapemeasure protein
Nb: Tapemeasure protein
Nc: Tapemeasure protein
Oa: Baseplate hub, gp25
Ob: Baseplate hub, gp25
Oc: Baseplate hub, gp25
Pa: Tail spike, gp29
Pb: Tail spike, gp29
Pc: Tail spike, gp29
Qa: Tail wing brush, gp33
Qb: Tail wing brush, gp33
Qc: Tail wing brush, gp33
Ra: Tail wing arm, gp31
Rb: Tail wing arm, gp31
Rc: Tail wing arm, gp31
Rd: Tail wing arm, gp31
Re: Tail wing arm, gp31
Rf: Tail wing arm, gp31
Sa: Tail wing base, gp30
Sb: Tail wing base, gp30
Sc: Tail wing base, gp30


Theoretical massNumber of molelcules
Total (without water)1,941,66645
Polymers1,941,66645
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 45 molecules JaJbJcJdJeJfKaKbKcLaLbLcLdLeLfLgLhLiMaMbMcMdMeMfNaNbNcOaObOc...

#1: Protein
Tail tube, gp19


Mass: 30170.271 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A2
#2: Protein Tail collar spacer, gp6


Mass: 9696.724 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: A0A345MFL2
#3: Protein
Tail collar fibers, gp4


Mass: 36723.973 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0B7
#4: Protein
Tail tip cage, gp23


Mass: 74357.398 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B098
#5: Protein Tapemeasure protein


Mass: 84842.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B099
#6: Protein Baseplate hub, gp25


Mass: 67065.172 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B096
#7: Protein Tail spike, gp29


Mass: 64056.230 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B092
#8: Protein Tail wing brush, gp33


Mass: 24772.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B088
#9: Protein
Tail wing arm, gp31


Mass: 11315.524 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: A0A345MFN8
#10: Protein Tail wing base, gp30


Mass: 54931.043 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B091

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium phage Bxb1 / Type: VIRUS
Details: Tail tip complex of Bxb1, containing ten protein subunit types. This is a composite map, and related entries for consensus and locally refined maps are noted.
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21YES
Source (natural)Organism: Mycobacterium phage Bxb1 (virus) / Strain: Mycobacterium phage Bxb1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Virus shellName: Mycobacteriophage Bxb1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
21 mMMagnesium sulfateMgSO41
368.44 mMSodium chlorideNaCl1
41 mMCalcium chlorideCaCl21
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22280 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005103878
ELECTRON MICROSCOPYf_angle_d0.644141916
ELECTRON MICROSCOPYf_dihedral_angle_d6.12714335
ELECTRON MICROSCOPYf_chiral_restr0.04715836
ELECTRON MICROSCOPYf_plane_restr0.00618732

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