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- PDB-9d9w: Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model -

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Basic information

Entry
Database: PDB / ID: 9d9w
TitleMycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Components
  • Major capsid protein
  • Portal protein
KeywordsVIRAL PROTEIN / Bacteriophage / Mycobacteriophage Bxb1 / capsid / portal / VIRUS
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / : / Phage capsid / Phage capsid family / virion component / Major capsid protein / Portal protein
Function and homology information
Biological speciesMycobacterium phage Bxb1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 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 1.2Apr 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 1.3Jun 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
Aa: Major capsid protein
Ab: Major capsid protein
Ac: Major capsid protein
Ad: Major capsid protein
Ae: Major capsid protein
Af: Major capsid protein
Ba: Major capsid protein
Bb: Major capsid protein
Bc: Major capsid protein
Bd: Major capsid protein
Be: Major capsid protein
Bf: Major capsid protein
Ca: Major capsid protein
Cb: Major capsid protein
Cc: Major capsid protein
Cd: Major capsid protein
Ce: Major capsid protein
Cf: Major capsid protein
Da: Major capsid protein
Db: Major capsid protein
Dc: Major capsid protein
Dd: Major capsid protein
De: Major capsid protein
Df: Major capsid protein
Ea: Major capsid protein
Eb: Major capsid protein
Ec: Major capsid protein
Ed: Major capsid protein
Ee: Major capsid protein
Ef: Major capsid protein
Fa: Portal protein
Fb: Portal protein
Fc: Portal protein
Fd: Portal protein
Fe: Portal protein
Ff: Portal protein
Fg: Portal protein
Fh: Portal protein
Fi: Portal protein
Fj: Portal protein
Fk: Portal protein
Fl: Portal protein


Theoretical massNumber of molelcules
Total (without water)1,902,12942
Polymers1,902,12942
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

#1: Protein ...
Major capsid protein


Mass: 41875.461 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A7
#2: Protein
Portal protein


Mass: 53822.113 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0B0
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: Portal and connector complex of Bxb1, containing five 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
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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 33132 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006133098
ELECTRON MICROSCOPYf_angle_d0.695181460
ELECTRON MICROSCOPYf_dihedral_angle_d6.2518457
ELECTRON MICROSCOPYf_chiral_restr0.04520807
ELECTRON MICROSCOPYf_plane_restr0.00623804

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