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- EMDB-21123: Actinobacteriophage Patience -

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Basic information

Entry
Database: EMDB / ID: EMD-21123
TitleActinobacteriophage Patience
Map dataActinobacteriophage Patience
Sample
  • Virus: Mycobacterium phage Patience (virus)
Biological speciesMycobacterium phage Patience (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsPodgorski JM / Calabrese J / Alexandrescu L / Jacobs-Sera D / Pope W / Hatfull G / White SJ
CitationJournal: Viruses / Year: 2020
Title: Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins.
Authors: Jennifer Podgorski / Joshua Calabrese / Lauren Alexandrescu / Deborah Jacobs-Sera / Welkin Pope / Graham Hatfull / Simon White /
Abstract: Here, we describe the structure of three actinobacteriophage capsids that infect . The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each ...Here, we describe the structure of three actinobacteriophage capsids that infect . The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each bacteriophage uses the HK97-fold to form their capsid. One bacteriophage, Rosebush, may have a novel variation of the HK97-fold. Four novel accessory proteins that form the capsid head along with the major capsid protein were identified. Two of the accessory proteins were minor capsid proteins and showed some homology, based on bioinformatic analysis, to the TW1 bacteriophage. The remaining two accessory proteins are decoration proteins that are located on the outside of the capsid and do not resemble any previously described bacteriophage decoration protein. SDS-PAGE and mass spectrometry was used to identify the accessory proteins and bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.
History
DepositionDec 15, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21123.png

Downloads & links

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Map

FileDownload / File: emd_21123.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActinobacteriophage Patience
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 400 pix.
= 880. Å		2.2 Å/pix.
x 400 pix.
= 880. Å		2.2 Å/pix.
x 400 pix.
= 880. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.028914746 - 0.096891165
Average (Standard dev.)0.005092776 (±0.013399097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 880.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z880.000880.000880.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0290.0970.005

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Supplemental data

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Mask #1

Fileemd_21123_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unpolished map

Fileemd_21123_additional.map
AnnotationUnpolished map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unpolished map

Fileemd_21123_additional_1.map
AnnotationUnpolished map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_21123_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_21123_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium phage Patience

EntireName: Mycobacterium phage Patience (virus)
Components
  • Virus: Mycobacterium phage Patience (virus)

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Supramolecule #1: Mycobacterium phage Patience

SupramoleculeName: Mycobacterium phage Patience / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Grown in host Mycobacterium smegmatis and cesium chloride-purified
NCBI-ID: 1074308 / Sci species name: Mycobacterium phage Patience / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / 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

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris Base
10.0 mMMgSO4Magnesium sulfate
68.0 mMNaClSodium chloride
1.0 mMCaCl2Calcium chloride
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was multiplexed with two other bacteriophages.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 996 / Average exposure time: 1.6 sec. / Average electron dose: 17.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3461
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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