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- EMDB-61659: Capsid structure of Escherichia phage Mu -

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Basic information

Entry
Database: EMDB / ID: EMD-61659
TitleCapsid structure of Escherichia phage Mu
Map data
Sample
  • Complex: Escherichia phage Mu
    • Protein or peptide: Major capsid protein
Keywordscapsid / phage / VIRAL PROTEIN
Function / homologyviral capsid, major subunit / Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT / host cell cytoplasm / Major capsid protein
Function and homology information
Biological speciesEscherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhou JQ / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: J Virol / Year: 2025
Title: structures of the contractile nanomachine myophage Mu in both its extended and contracted states.
Authors: Junquan Zhou / Liwen Wang / Hao Xiao / Wenyuan Chen / Zhonghua Liu / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic ...Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic engineering research. Nevertheless, a comprehensive understanding of the entire structure and contractile mechanisms of Mu remains elusive. Using cryo-electron microscopy (cryo-EM), we resolved the asymmetric structures of Mu in both its extended and contracted states, the latter of which lacked the tail baseplate, at near-atomic resolutions. We built the atomic models for the extended Mu, encompassing the head, the connector complex, the tail, and the simple baseplate. It is noteworthy that we identified the position and structure of the tail tube initiator protein gp43 (referred to as the DNA circularization protein). The protein gp43 plays a crucial role not only in the baseplate assembly and DNA circularization but also in stabilizing the wedge-hub connection and mediating tail contraction. Except for the baseplate structure, the structural comparison of Mu in its extended and contracted states revealed that only the tail sheath protein gp39 and the C-terminus of the tail terminator protein gp37 undergo notable conformational changes to accommodate the tail contraction, whereas the remaining protein components remained unchanged. Our structures exhibited conserved properties among the majority of myophages, thereby providing valuable insights into the contraction mechanisms across myophages and contractile injection systems (CISs).
IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in ...IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in both its extended and contracted states. The comparison of the two structures allows for the illustration of detailed conformational changes of the head-to-tail complex during the process of tail contraction. The contraction mechanism of Mu is highly conserved and widely adapted to all contractile nanomachines that share common structural features with Mu.
History
DepositionSep 24, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61659.png

Downloads & links

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Map

FileDownload / File: emd_61659.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-23.625069 - 45.055186999999997
Average (Standard dev.)0.016653655 (±1.7642603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61659_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_61659_half_map_2.map
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Sample components

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Entire : Escherichia phage Mu

EntireName: Escherichia phage Mu (virus)
Components
  • Complex: Escherichia phage Mu
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Escherichia phage Mu

SupramoleculeName: Escherichia phage Mu / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Mu (virus)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 34.197691 KDa
SequenceString: MIVTPASIKA LMTSWRKDFQ GGLEDAPSQY NKIAMVVNSS TRSNTYGWLG KFPTLKEWVG KRTIQQMEAH GYSIANKTFE GTVGISRDD FEDDNLGIYA PIFQEMGRSA AVQPDELIFK LLKDGFTQPC YDGQNFFDKE HPVYPNVDGT GSAVNTSNIV E QDSFSGLP ...String:
MIVTPASIKA LMTSWRKDFQ GGLEDAPSQY NKIAMVVNSS TRSNTYGWLG KFPTLKEWVG KRTIQQMEAH GYSIANKTFE GTVGISRDD FEDDNLGIYA PIFQEMGRSA AVQPDELIFK LLKDGFTQPC YDGQNFFDKE HPVYPNVDGT GSAVNTSNIV E QDSFSGLP FYLLDCSRAV KPLIFQERRK PELVARTRID DDHVFMDNEF LFGASTRRAA GYGFWQMAVA VKGDLTLDNL WK GWQLMRS FEGDGGKKLG LKPTHIVVPV GLEKAAEQLL NRELFADGNT TVSNEMKGKL QLVVADYL

UniProtKB: Major capsid 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55035
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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