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- EMDB-22250: The Heterotetramers of Holin-Antiholin -

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Basic information

Entry
Database: EMDB / ID: EMD-22250
TitleThe Heterotetramers of Holin-Antiholin
Map datasRI-sT heterotetramers
Sample
  • Complex: The heterotetramers of holin-antiholin
Function / homology
Function and homology information


: / host cell periplasmic space / pore-forming activity / cytolysis / molecular function inhibitor activity / viral release from host cell by cytolysis / killing of cells of another organism / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Bacteriophage T4, GpT, holin / Bacteriophage T holin / Antiholin T4 type
Similarity search - Domain/homology
Holin / Antiholin / Holin / Antiholin
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsChang JY / Krieger I / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationA1863 United States
CitationJournal: J Mol Biol / Year: 2020
Title: The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition.
Authors: Inna V Krieger / Vladimir Kuznetsov / Jeng-Yih Chang / Junjie Zhang / Samir H Moussa / Ryland F Young / James C Sacchettini /
Abstract: Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, ...Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI-2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI-T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.
History
DepositionJun 29, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22250.png

Downloads & links

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Map

FileDownload / File: emd_22250.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationsRI-sT heterotetramers
Voxel sizeX=Y=Z: 3 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.123726204 - 0.3381928
Average (Standard dev.)0.004112559 (±0.025292465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-0.1240.3380.004

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Supplemental data

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Sample components

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Entire : The heterotetramers of holin-antiholin

EntireName: The heterotetramers of holin-antiholin
Components
  • Complex: The heterotetramers of holin-antiholin

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Supramolecule #1: The heterotetramers of holin-antiholin

SupramoleculeName: The heterotetramers of holin-antiholin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia phage T4 (virus)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35432
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6pxe

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