[English] 日本語
Yorodumi
- EMDB-63436: Bacteriophage Mycofy1 distal head-to-tail interface (C6 symmetry) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63436
TitleBacteriophage Mycofy1 distal head-to-tail interface (C6 symmetry)
Map data
Sample
  • Virus: Mycolicibacterium phage Mycofy1 (virus)
    • Protein or peptide: Head-to-tail stopper
    • Protein or peptide: Terminator protein gp11
    • Protein or peptide: Major tail protein
KeywordsMycobacterium / bacteriophage / prolate head / head-to-tail interface / connector protein / terminator protein / tail tube protein / VIRUS / VIRAL PROTEIN
Function / homologyMajor tail protein / Head-to-tail stopper
Function and homology information
Biological speciesMycolicibacterium phage Mycofy1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 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

-
Structure visualization

Supplemental images

emd_63436.png

Downloads & links

-
Map

FileDownload / File: emd_63436.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.019720891 - 0.04609217
Average (Standard dev.)-0.00012793034 (±0.0025628854)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_63436_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63436_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63436_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mycolicibacterium phage Mycofy1

EntireName: Mycolicibacterium phage Mycofy1 (virus)
Components
  • Virus: Mycolicibacterium phage Mycofy1 (virus)
    • Protein or peptide: Head-to-tail stopper
    • Protein or peptide: Terminator protein gp11
    • Protein or peptide: Major tail protein

-
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)

-
Macromolecule #1: Head-to-tail stopper

MacromoleculeName: Head-to-tail stopper / 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 Q854Y9.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 13.696388 KDa
SequenceString:
MSEEFGGQVV ALVSVAETGV PGWGGLKAKA RTTTRQPGVH FRPASSTETP DGQTNVATEV WKLTAPPTAA VLAAKPGGEL VYDGTEHPE SLDLDSAAGR AATFRVDGPI MPKYDLAGQV HHVTIMCKRQ AG

UniProtKB: Head-to-tail stopper

-
Macromolecule #2: Terminator protein gp11

MacromoleculeName: Terminator protein gp11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 15.704601 KDa
SequenceString:
MTMADLHDQD APDEEDFVVC WMQPVMRTAV ERDIDAELPF CEVTRIDGAD DPEAGTDDPV IQLDFYALGA EAAKAAAKQG HRRMLFLFR NFPTVTLSDG TLADLDFGET LIKPSRMAFE HDQIVRYTAR YQLGTSYVAV P

-
Macromolecule #3: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 3
Details: Sequence reference for Mycolicibacterium phage Mycofy1 is not available at the time of biocuration. Current sequence reference is from UniProt id A0A0A7RVP8.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Molecular weightTheoretical: 29.029006 KDa
SequenceString: MTQPLTGTTP AAGGYTTVDN RLQGGHRTGL IAVAFRDALG TSTNISPHNA NGSVRWSPLA QDGQLRDDLF AHRLENGVWV ENTNPNEGW YLAGAFGEGN GPSSRPSIDT DDQMIEQSNW PFESDITKQD EPFTFQALQN LYPAIQRLAN NLPLSDANGN P LVELPGEA ...String:
MTQPLTGTTP AAGGYTTVDN RLQGGHRTGL IAVAFRDALG TSTNISPHNA NGSVRWSPLA QDGQLRDDLF AHRLENGVWV ENTNPNEGW YLAGAFGEGN GPSSRPSIDT DDQMIEQSNW PFESDITKQD EPFTFQALQN LYPAIQRLAN NLPLSDANGN P LVELPGEA DGFSQPVDAE KIGRQFLLYG IRKKEGRYLY EVDAYDLAYL NNKGERKFGK RGTAAELTFK PEPSGYFMAM VD GEYKPII KHTFIGGPAW DALAGDGS

UniProtKB: Major tail protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 22074 / Details: Manual picking
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more