[English] 日本語
Yorodumi
- EMDB-62462: Neck structure of bacteriophage Mu in contracted state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62462
TitleNeck structure of bacteriophage Mu in contracted state
Map data
Sample
  • Complex: Escherichia phage Mu
    • Protein or peptide: Portal protein
    • Protein or peptide: Gene product J
Keywordsportal / adaptor / phage / VIRAL PROTEIN
Function / homologyProtein of unknown function DUF935 / Portal protein of Mu bacteriophage / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral capsid / host cell cytoplasm / Gene product J / Portal protein
Function and homology information
Biological speciesEscherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu HR / Zhou JQ
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
DepositionNov 19, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62462.png

Downloads & links

-
Map

FileDownload / File: emd_62462.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-8.531354 - 17.370954999999999
Average (Standard dev.)0.008797312 (±0.83585554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62462_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62462_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage Mu

EntireName: Escherichia phage Mu (virus)
Components
  • Complex: Escherichia phage Mu
    • Protein or peptide: Portal protein
    • Protein or peptide: Gene product J

-
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)

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 56.952305 KDa
SequenceString: MGRILDISGQ PFDFDDEMQS RSDELAMVMK RTQEHPSSGV TPNRAAQMLR DAERGDLTAQ ADLAFDMEEK DTHLFSELSK RRLAIQALE WRIAPARDAS AQEKKDADML NEYLHDAAWF EDALFDAGDA ILKGYSMQEI EWGWLGKMRV PVALHHRDPA L FCANPDNL ...String:
MGRILDISGQ PFDFDDEMQS RSDELAMVMK RTQEHPSSGV TPNRAAQMLR DAERGDLTAQ ADLAFDMEEK DTHLFSELSK RRLAIQALE WRIAPARDAS AQEKKDADML NEYLHDAAWF EDALFDAGDA ILKGYSMQEI EWGWLGKMRV PVALHHRDPA L FCANPDNL NELRLRDASY HGLELQPFGW FMHRAKSRTG YVGTNGLVRT LIWPFIFKNY SVRDFAEFLE IYGLPMRVGK YP TGSTNRE KATLMQAVMD IGRRAGGIIP MGMTLDFQSA ADGQSDPFMA MIGWAEKAIS KAILGGTLTT EAGDKGARSL GEV HDEVRR EIRNADVGQL ARSINRDLIY PLLALNSDST IDINRLPGIV FDTSEAGDIT ALSDAIPKLA AGMRIPVSWI QEKL HIPQP VGDEAVFTIQ PVVPDNGSQK EAALSAEDIP QEDDIDRMGV SPEDWQRSVD PLLKPVIFSV LKDGPEAAMN KAASL YPQM DDAELIDMLT RAIFVADIWG RLDAAADH

UniProtKB: Portal protein

-
Macromolecule #2: Gene product J

MacromoleculeName: Gene product J / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 15.742675 KDa
SequenceString:
MNYATVNDLC ARYTRTRLDI LTRPKTADGQ PDDAVAEQAL ADASAFIDGY LAARFVLPLT VVPSLLKRQC CVVAWFYLNE SQPTEQITA TYRDTVRWLE QVRDGKTDPG VESRTAASPE GEDLVQVQSD PPVFSRKQKG FI

UniProtKB: Gene product J

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42000
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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