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- PDB-8jan: In situ structures of the ultra-long extended tail of Myoviridae ... -

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Basic information

Entry
Database: PDB / ID: 8jan
TitleIn situ structures of the ultra-long extended tail of Myoviridae phage P1
Components
  • BplB
  • Gp22
  • Gp24
KeywordsVIRAL PROTEIN / Complex / phage / VIRUS
Function / homologyGp24 / Gp22 / BplB
Function and homology information
Biological speciesEscherichia phage P1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou, J.Q. / Liu, H.R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: Viruses / Year: 2023
Title: In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1.
Authors: Fan Yang / Liwen Wang / Junquan Zhou / Hao Xiao / Hongrong Liu /
Abstract: The phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near- ...The phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the tail.
History
DepositionMay 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: BplB
b: BplB
c: BplB
d: BplB
e: BplB
f: BplB
g: BplB
h: BplB
i: BplB
j: BplB
k: BplB
l: BplB
m: Gp22
n: Gp22
o: Gp22
p: Gp22
q: Gp22
r: Gp22
s: Gp22
t: Gp22
u: Gp22
v: Gp22
w: Gp22
x: Gp22
y: Gp24
z: Gp24
A: Gp24
B: Gp24
C: Gp24
D: Gp24


Theoretical massNumber of molelcules
Total (without water)1,083,42330
Polymers1,083,42330
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
BplB / Tail tube protein


Mass: 18827.127 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: Q71TM5
#2: Protein
Gp22 / Tail sheath protein


Mass: 56989.246 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: Q71TB2
#3: Protein
Gp24 / Tail terminator protein


Mass: 28937.674 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: Q71T90

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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 P1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage P1 (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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32031 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00376584
ELECTRON MICROSCOPYf_angle_d0.504104136
ELECTRON MICROSCOPYf_dihedral_angle_d4.2710590
ELECTRON MICROSCOPYf_chiral_restr0.04412012
ELECTRON MICROSCOPYf_plane_restr0.00413488

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