[English] 日本語
Yorodumi
- PDB-9ki1: Baseplate structure of Escherichia phage Mu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ki1
TitleBaseplate structure of Escherichia phage Mu
Components
  • (Baseplate protein ...) x 3
  • Baseplate hub protein gp44
  • Baseplate puncturing device gp45
  • DNA circularization protein N
  • Probable tape measure protein
  • Tail fiber protein S
  • Tail sheath protein
  • Tail tube protein
KeywordsVIRAL PROTEIN / phage / sheath / tube
Function / homology
Function and homology information


viral genome circularization / symbiont-mediated evasion of DNA end degradation by host / viral tropism switching / virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / adhesion receptor-mediated virion attachment to host cell ...viral genome circularization / symbiont-mediated evasion of DNA end degradation by host / viral tropism switching / virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / adhesion receptor-mediated virion attachment to host cell / virion component / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / DNA binding / metal ion binding
Similarity search - Function
Bacteriophage Mu, Baseplate protein gp46 / : / Phage protein GP46 / Bacteriophage lambda, Tail fiber protein, repeat-2 / DNA circulation, N-terminal / Phage-associated protein Gp45 / : / : / Phage tail fibre repeat / Bacteriophage Mu Gp45, N-terminal ...Bacteriophage Mu, Baseplate protein gp46 / : / Phage protein GP46 / Bacteriophage lambda, Tail fiber protein, repeat-2 / DNA circulation, N-terminal / Phage-associated protein Gp45 / : / : / Phage tail fibre repeat / Bacteriophage Mu Gp45, N-terminal / DNA circularisation protein N-terminus / Mu phage baseplate assembly protein GpP, fourth domain / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / : / : / Mu phage baseplate assembly protein GpP-like, N-terminal / Baseplate hub protein gp44-like, second domain / Bacteriophage Mu, GpM, tail tube / Phage tail tube protein / Tail sheath protein / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Tape measure protein N-terminal / Tape measure protein / Phage baseplate assembly protein V/Gp45 / Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / : / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Baseplate protein J-like / Baseplate J-like protein / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
: / DNA circularization protein N / Baseplate hub protein gp44 / Tail sheath protein / Tail tube protein / Tail fiber protein S / Baseplate protein gp48 / Baseplate protein gp47 / Baseplate protein gp46 / Baseplate puncturing device gp45 / Probable tape measure protein
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou, J.Q. / Liu, H.R.
Funding support China, 3items
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 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: DNA circularization protein N
1: Tail sheath protein
2: Tail sheath protein
3: Tail sheath protein
4: Tail tube protein
5: Tail tube protein
6: Tail tube protein
7: Tail tube protein
8: Tail tube protein
9: Tail tube protein
A: Baseplate protein gp46
B: Baseplate protein gp46
C: Baseplate protein gp46
D: Baseplate protein gp46
E: Baseplate protein gp46
F: Baseplate protein gp46
G: Baseplate hub protein gp44
H: Baseplate protein gp47
I: Baseplate protein gp47
J: Baseplate protein gp47
K: Baseplate protein gp47
L: Baseplate protein gp47
M: Baseplate protein gp47
N: Baseplate hub protein gp44
O: Baseplate protein gp47
P: Baseplate protein gp47
Q: Baseplate protein gp47
R: Baseplate protein gp47
S: Baseplate protein gp47
T: Baseplate protein gp47
U: Baseplate hub protein gp44
V: Baseplate puncturing device gp45
W: Baseplate puncturing device gp45
X: Baseplate puncturing device gp45
a: Baseplate protein gp48
b: Baseplate protein gp48
c: Baseplate protein gp48
d: Baseplate protein gp48
e: Baseplate protein gp48
f: Baseplate protein gp48
g: Probable tape measure protein
h: Probable tape measure protein
i: Probable tape measure protein
j: Tail fiber protein S
k: Tail fiber protein S
l: Tail fiber protein S
m: Tail fiber protein S
n: Tail fiber protein S
o: Tail fiber protein S
p: Tail fiber protein S
q: Tail fiber protein S
r: Tail fiber protein S
s: DNA circularization protein N
t: DNA circularization protein N
u: DNA circularization protein N
v: DNA circularization protein N
w: DNA circularization protein N
x: Tail sheath protein
y: Tail sheath protein
z: Tail sheath protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,304,56362
Polymers2,304,46760
Non-polymers962
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 36 molecules 0stuvw123xyz456789GNUVWXghijkl...

#1: Protein
DNA circularization protein N / tube initiator protein gp43 / 64 kDa virion protein / Gene product 43 / gp43 / Gene product N / gpN


Mass: 52085.984 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: P08557
#2: Protein
Tail sheath protein / sheath protein gp39 / TSP / Gene product 39 / gp39 / Gene product L / gpL


Mass: 53132.508 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: P79678
#3: Protein
Tail tube protein / tube protein gp40 / TTP / Gene product 40 / gp40 / Gene product M / gpM


Mass: 12840.470 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: P79679
#5: Protein Baseplate hub protein gp44 / hub protein gp44 / 43 kDa tail protein / Gene product 44 / gp44 / Gene product P / gpP


Mass: 41840.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: P08558
#7: Protein Baseplate puncturing device gp45 / spike protein gp45 / Baseplate spike protein / Gene product 45 / gp45 / Gene product Q / gpQ


Mass: 21720.525 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V4
#9: Protein Probable tape measure protein / tape measure protein gp42 / TMP / Gene product 42 / gp42 / Gene product Y / gpY


Mass: 73682.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V6
#10: Protein
Tail fiber protein S / fiber protein gp49 / Gene product 49 / gp49 / Gene product S / gpS


Mass: 55412.551 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V0

-
Baseplate protein ... , 3 types, 24 molecules ABCDEFHIJKLMOPQRSTabcdef

#4: Protein
Baseplate protein gp46 / sheath initiator protein gp46 / Gene product 46 / gp46 / Gene product V / gpV


Mass: 16340.159 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V3
#6: Protein
Baseplate protein gp47 / wedge protein gp47-i / Gene product 47 / gp47 / Gene product W / gpW


Mass: 38724.578 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V2
#8: Protein
Baseplate protein gp48 / wedge protein gp48 / Gene product 48 / gp48 / Gene product R / gpR


Mass: 20489.059 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V1

-
Non-polymers , 2 types, 2 molecules

#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Escherichia phage Mu / Type: VIRUS / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Escherichia phage Mu (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46000 / Symmetry type: POINT

+
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