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- EMDB-63432: Top cap of bacteriophage Mycofy1 mature head (C5 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-63432
TitleTop cap of bacteriophage Mycofy1 mature head (C5 symmetry)
Map data
Sample
  • Virus: Mycolicibacterium phage Mycofy1 (virus)
    • Protein or peptide: Phage capsid-like C-terminal domain-containing protein
KeywordsMycobacterium / bacteriophage / prolate head / major capsid protein / VIRUS / VIRAL PROTEIN
Function / homology: / Phage capsid / Phage capsid family / virion component / Phage capsid-like C-terminal domain-containing protein
Function and homology information
Biological speciesMycolicibacterium phage Mycofy1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLi X / Shao Q / Li L / Xie L / Ruan Z / Fang Q
Funding support China, 2 items
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, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63432.png

Downloads & links

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Map

FileDownload / File: emd_63432.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 500 pix.
= 823.2 Å		1.65 Å/pix.
x 500 pix.
= 823.2 Å		1.65 Å/pix.
x 500 pix.
= 823.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6464 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0203
Minimum - Maximum-0.05103687 - 0.09774582
Average (Standard dev.)-0.000042803862 (±0.0052794633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 823.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63432_msk_1.map
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Half map: #2

Fileemd_63432_half_map_1.map
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Half map: #1

Fileemd_63432_half_map_2.map
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Sample components

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Entire : Mycolicibacterium phage Mycofy1

EntireName: Mycolicibacterium phage Mycofy1 (virus)
Components
  • Virus: Mycolicibacterium phage Mycofy1 (virus)
    • Protein or peptide: Phage capsid-like C-terminal domain-containing protein

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Supramolecule #1: Mycolicibacterium phage Mycofy1

SupramoleculeName: Mycolicibacterium phage Mycofy1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3349809 / Sci species name: Mycolicibacterium phage Mycofy1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Phage capsid-like C-terminal domain-containing protein

MacromoleculeName: Phage capsid-like C-terminal domain-containing protein
type: protein_or_peptide / ID: 1
Details: Sequence reference for Mycolicibacterium phage Mycofy1 is not available at the time of biocuration. Current sequence reference is from UniProt id Q854Z2.
Number of copies: 54 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 59.777262 KDa
SequenceString: MNTLDTLPVH PRTGLRAIGM GKRGPIWPVM GASDDHKDDA PTLTYSQARN RADEVHARME QIAELDKPTD EENEEFRALG AEFDSLVNH MSRLERAAEL ARVRSTHEQI GKPQSGGQRR MRVEAGSSQG GRGDYDRDAI LEPDSIEDCR FRDPWNLSEM R TFGRDAEE ...String:
MNTLDTLPVH PRTGLRAIGM GKRGPIWPVM GASDDHKDDA PTLTYSQARN RADEVHARME QIAELDKPTD EENEEFRALG AEFDSLVNH MSRLERAAEL ARVRSTHEQI GKPQSGGQRR MRVEAGSSQG GRGDYDRDAI LEPDSIEDCR FRDPWNLSEM R TFGRDAEE VKGELRARAL SAIEKMQGAS DNVRAAATHI IERFDDEDST LARQCLATSS PAYLRAWSKM ARNPHAAILT EE EKRAINE VRAMGLTKAD GGYLVPFQLD PTVIITSNGS LNDIRRFARQ VVATGDVWHG VSSAAVQWSW DAEFEEVSDD SPE FGQPEI PVKKAQGFVP ISIEALQDEA NVTETVALLF AEGKDELEAV TLTTGTGQGN QPTGIVTALA GTAAEIAPVT AETF ALADV YAVYEQLAAR HRRQGAWLAN NLIYNKIRQF DTQGGAGLWT TIGNGEPSQL LGRPVGEAEA MDANWNTSAS ADNFV LLYG NFQNYVIADR IGMTVEFIPH LFGTNRRPNG SRGWFAYYRM GADVVNPNAF RLLNVETAS

UniProtKB: Phage capsid-like C-terminal domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 5.09 sec. / Average electron dose: 25.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22074 / Details: Manual picking
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 19765
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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