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- PDB-9khx: Neck structure of Escherichia phage Mu -

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Basic information

Entry
Database: PDB / ID: 9khx
TitleNeck structure of Escherichia phage Mu
Components
  • Gene product J
  • Portal protein
KeywordsVIRAL PROTEIN / portal / adaptor / phage
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene product J
X: Portal protein
B: Gene product J
C: Gene product J
D: Gene product J
E: Gene product J
F: Gene product J
G: Gene product J
H: Gene product J
I: Gene product J
J: Gene product J
K: Gene product J
L: Gene product J
M: Portal protein
N: Portal protein
O: Portal protein
P: Portal protein
Q: Portal protein
R: Portal protein
S: Portal protein
T: Portal protein
U: Portal protein
V: Portal protein
W: Portal protein


Theoretical massNumber of molelcules
Total (without water)872,34024
Polymers872,34024
Non-polymers00
Water00
1


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

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Components

#1: Protein
Gene product J / adaptor protein gp36 / gpJ / Gene product 36 / gp36


Mass: 15742.675 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1V9
#2: Protein
Portal protein / portal protein gp29 / Gene product 29 / gp29 / Gene product H / gpH / Head-tail connector


Mass: 56952.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Mu (virus) / References: UniProt: Q9T1W5
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Escherichia phage Mu / Type: COMPLEX / Entity ID: all / 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

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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)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55035 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00248756
ELECTRON MICROSCOPYf_angle_d0.45166048
ELECTRON MICROSCOPYf_dihedral_angle_d2.8436684
ELECTRON MICROSCOPYf_chiral_restr0.0377212
ELECTRON MICROSCOPYf_plane_restr0.0048736

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