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- PDB-9lwa: Bacteriophage Mycofy1 distal head-to-tail interface (C6 symmetry) -

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Basic information

Entry
Database: PDB / ID: 9lwa
TitleBacteriophage Mycofy1 distal head-to-tail interface (C6 symmetry)
Components
  • Head-to-tail stopper
  • Major tail protein
  • Terminator protein gp11
KeywordsVIRAL PROTEIN / Mycobacterium / bacteriophage / prolate head / head-to-tail interface / connector protein / terminator protein / tail tube protein / VIRUS
Function / homologyMajor tail protein / Head-to-tail stopper
Function and homology information
Biological speciesMycolicibacterium phage Mycofy1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsLi, X. / Shao, Q. / Li, L. / Xie, L. / Ruan, Z. / Fang, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Shenzhen Science and Technology ProgramJCYJ20240813180500001 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM Reveals Structural Diversity in Prolate-headed Mycobacteriophage Mycofy1.
Authors: Xiangyun Li / Qianqian Shao / Lin Li / Linlin Xie / Zhiyang Ruan / Qianglin Fang /
Abstract: Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that ...Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that Mycofy1 possesses a prolate head and a long non-contractile tail. We determined structures of its head, head-to-tail interface, terminator, and tail tube to resolutions of ∼3.5 Å. Unexpectedly, we identified two distinct types of prolate head structures, exhibiting a 36° relative rotation in the top cap region. Additionally, the head-to-tail interface demonstrated flexibility. Our structures provide high-resolution cryo-EM data of a mycobacteriophage with a prolate head, as well as detailed structural information of the head-to-tail interface and head-proximal tail region in this phage group. These findings advance our understanding of assembly mechanisms in tailed bacteriophages.
History
DepositionFeb 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Head-to-tail stopper
B: Terminator protein gp11
C: Major tail protein


Theoretical massNumber of molelcules
Total (without water)58,4303
Polymers58,4303
Non-polymers00
Water00
1
A: Head-to-tail stopper
B: Terminator protein gp11
C: Major tail protein
x 6


Theoretical massNumber of molelcules
Total (without water)350,58018
Polymers350,58018
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Head-to-tail stopper / Stopper protein gp9


Mass: 13696.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Mycolicibacterium phage Mycofy1 is not available at the time of biocuration. Current sequence reference is from UniProt id Q854Y9.
Source: (natural) Mycolicibacterium phage Mycofy1 (virus) / References: UniProt: Q854Y9
#2: Protein Terminator protein gp11


Mass: 15704.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium phage Mycofy1 (virus)
#3: Protein Major tail protein / Tail tube protein gp12


Mass: 29029.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Mycolicibacterium phage Mycofy1 is not available at the time of biocuration. Current sequence reference is from UniProt id A0A0A7RVP8.
Source: (natural) Mycolicibacterium phage Mycofy1 (virus) / References: UniProt: A0A0A7RVP8
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: Mycolicibacterium phage Mycofy1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.09 sec. / Electron dose: 25.7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.19.2_4158:model refinement
3EPUimage acquisition
5CTFFIND4CTF correction
10RELION4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22074 / Details: Manual picking
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12594 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024110
ELECTRON MICROSCOPYf_angle_d0.4915594
ELECTRON MICROSCOPYf_dihedral_angle_d4.046562
ELECTRON MICROSCOPYf_chiral_restr0.039601
ELECTRON MICROSCOPYf_plane_restr0.005753

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