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- EMDB-9392: Bacteriophage L virion -

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Basic information

Entry
Database: EMDB / ID: EMD-9392
TitleBacteriophage L virion
Map data1/8th of the virion for phage L-segmentation shows capsid protein only
Sample
  • Virus: Enterobacteria phage L (virus)
Function / homologyDec protein
Function and homology information
Biological speciesEnterobacteria phage L (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsParent KN / Schrad JR
CitationJournal: Elife / Year: 2019
Title: The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy.
Authors: Rebecca L Newcomer / Jason R Schrad / Eddie B Gilcrease / Sherwood R Casjens / Michael Feig / Carolyn M Teschke / Andrei T Alexandrescu / Kristin N Parent /
Abstract: The major coat proteins of dsDNA tailed phages (order ) and herpesviruses form capsids by a mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, followed by ...The major coat proteins of dsDNA tailed phages (order ) and herpesviruses form capsids by a mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, followed by expansion and stabilization of the capsid. These viruses have evolved diverse strategies to fortify their capsids, such as non-covalent binding of auxiliary 'decoration' (Dec) proteins. The Dec protein from the P22-like phage L has a highly unusual binding strategy that distinguishes between nearly identical three-fold and quasi-three-fold sites of the icosahedral capsid. Cryo-electron microscopy and three-dimensional image reconstruction were employed to determine the structure of native phage L particles. NMR was used to determine the structure/dynamics of Dec in solution. The NMR structure and the cryo-EM density envelope were combined to build a model of the capsid-bound Dec trimer. Key regions that modulate the binding interface were verified by site-directed mutagenesis.
History
Header (metadata) releaseMay 2, 2018-
DepositionJan 4, 2019-
Map releaseMar 27, 2019-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9392.png

Downloads & links

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Map

FileDownload / File: emd_9392.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation1/8th of the virion for phage L-segmentation shows capsid protein only
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.26 Å/pix.
x 272 pix.
= 342.72 Å		1.26 Å/pix.
x 272 pix.
= 342.72 Å		1.26 Å/pix.
x 272 pix.
= 342.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.18 / Movie #1: 2.18
Minimum - Maximum-8.963733 - 17.443864999999999
Average (Standard dev.)0.000000000000033 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-136-136-136
Dimensions272272272
Spacing272272272
CellA=B=C: 342.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z272272272
origin x/y/z0.0000.0000.000
length x/y/z342.720342.720342.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-136-136-136
NX/NY/NZ272272272
MAP C/R/S321
start NC/NR/NS-136-136-136
NC/NR/NS272272272
D min/max/mean-8.96417.4440.000

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Supplemental data

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Additional map: single Dec trimer segmented from phage L virion map

Fileemd_9392_additional.map
Annotationsingle Dec trimer segmented from phage L virion map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage L

EntireName: Enterobacteria phage L (virus)
Components
  • Virus: Enterobacteria phage L (virus)

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Supramolecule #1: Enterobacteria phage L

SupramoleculeName: Enterobacteria phage L / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 45441 / Sci species name: Enterobacteria phage L / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 60 MDa
Virus shellShell ID: 1 / Name: coat protein / T number (triangulation number): 7

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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

Concentration1 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
10.0 mMMgCl2magnesium chloride
10.0 mMC4H11NO3Tris
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100.0 nm / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Detailsconcentration is 1x10^12 phage/mL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 0-53 / Number grids imaged: 1 / Number real images: 494 / Average exposure time: 2.0 sec. / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.49 µm / Nominal defocus min: 0.35 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsimages were motion corrected and also particles were corrected for damage compensation
CTF correctionSoftware - Name: Auto3DEM (ver. v4.01.07) / Details: estimated manually
Startup modelType of model: OTHER / Details: random model computation
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM (ver. v4.01.07) / Number images used: 7879
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Auto3DEM (ver. v4.01.07)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Auto3DEM (ver. v4.01.07)

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