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- EMDB-63435: Bacteriophage Mycofy1 proximal head-to-tail interface (C6 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-63435
TitleBacteriophage Mycofy1 proximal head-to-tail interface (C6 symmetry)
Map data
Sample
  • Virus: Mycolicibacterium phage Mycofy1 (virus)
    • Protein or peptide: Adaptor protein gp8
    • Protein or peptide: Portal protein
KeywordsMycobacterium / bacteriophage / prolate head / head-to-tail connector / portal protein / adaptor protein / VIRUS / VIRAL PROTEIN
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / viral capsid / Portal protein
Function and homology information
Biological speciesMycolicibacterium phage Mycofy1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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_63435.png

Downloads & links

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Map

FileDownload / File: emd_63435.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 240 pix.
= 329.28 Å		1.37 Å/pix.
x 240 pix.
= 329.28 Å		1.37 Å/pix.
x 240 pix.
= 329.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0124
Minimum - Maximum-0.037985623 - 0.06034382
Average (Standard dev.)-0.00007431746 (±0.0037255983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 329.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63435_msk_1.map
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Half map: #2

Fileemd_63435_half_map_1.map
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Half map: #1

Fileemd_63435_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: Adaptor protein gp8
    • Protein or peptide: Portal protein

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Supramolecule #1: Mycolicibacterium phage Mycofy1

SupramoleculeName: Mycolicibacterium phage Mycofy1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2, #1 / 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: Portal protein

MacromoleculeName: Portal 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 A0A0A7RVH8.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 50.525547 KDa
SequenceString: MRLIDRLLST RGAAQRMSID DYAHMLNEFA FNGIGYGFGG GVPRIQQTLA GPSTELAPDT FVGLATQAYQ ANGPVFACML VRQLVFSSV RFRWQRLRDG KPSDTFGSGD LQILETPWKG GTTQDMLSRM IQDADLAGNS YWTIVDGEFV RMRPDWVDVV V EERMVRGG ...String:
MRLIDRLLST RGAAQRMSID DYAHMLNEFA FNGIGYGFGG GVPRIQQTLA GPSTELAPDT FVGLATQAYQ ANGPVFACML VRQLVFSSV RFRWQRLRDG KPSDTFGSGD LQILETPWKG GTTQDMLSRM IQDADLAGNS YWTIVDGEFV RMRPDWVDVV V EERMVRGG RGERGGGQLG WRKVGYLYTE GGRQSGNEPV GFLAEDVVHF APIPDPLASY RGMSWLTPIL REIRADQAMS KH QAKFFDN GATVNLVIKH NPMADPAAVK KWADEVNSKH AGVDNAWKNL NLYPGADAEV VGSNLQEIDF KNVRGGGETR IAA AAGVPP VIVGLSEGLA AATYSNYGQA RRRLADGTAH PLWQNLSGCI GHVMPDMGPD VRLWYDADDV PFLREDEKDA ADIQ KVRAE TINTLITAGY EPDSVVAAVN SGDLRLLKHT GLTSVQLLPP GVSASAPSDT PTSGGADDNG N

UniProtKB: Portal protein

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Macromolecule #2: Adaptor protein gp8

MacromoleculeName: Adaptor protein gp8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 19.875471 KDa
SequenceString:
MAELKPDDLP AKVRGQFADN TEAQAAIDAV LAAARRWCGW HVSPVIVDDV MELDGPGGRV LSLPTLNLVS VSSVVELGHA LDVSTLDRS RRKGTLTKPY GRWTARDGAI VVTATHGFTE AEAADWRRAV VQLVGQRAQT SRPSADLKRK KIDDVEYEWF E TAVSVDAE LSAVFSPFRI LPSP

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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

MicroscopeTFS 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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12594
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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