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- EMDB-10238: Focused Classification of the vertex region of Bacteriophage PR77... -

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Basic information

Entry
Database: EMDB / ID: EMD-10238
TitleFocused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton
Map dataFocused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton
Sample
  • Complex: Bacteriophage PR772
Biological speciesEnterobacteria phage PR772 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsNarayana Reddy HK / Svenda M
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council628-20081109822-2010-6157, 822-2012-5260 and 828-2012-108 Sweden
European Research CouncilERC-291602 Sweden
Knut and Alice Wallenberg FoundationKAW-2011.081 Sweden
CitationJournal: Elife / Year: 2019
Title: Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture.
Authors: Hemanth Kn Reddy / Marta Carroni / Janos Hajdu / Martin Svenda /
Abstract: Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged ...Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
History
DepositionAug 19, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10238.png

Downloads & links

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Map

FileDownload / File: emd_10238.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused Classification of the vertex region of Bacteriophage PR772 showing the heteropentameric penton
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 432 pix.
= 915.84 Å		2.12 Å/pix.
x 432 pix.
= 915.84 Å		2.12 Å/pix.
x 432 pix.
= 915.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0365 / Movie #1: 0.0365
Minimum - Maximum-0.048992846 - 0.11597887
Average (Standard dev.)0.000009627039 (±0.0006884724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 915.83997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.122.122.12
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z915.840915.840915.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0490.1160.000

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Supplemental data

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Sample components

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Entire : Bacteriophage PR772

EntireName: Bacteriophage PR772
Components
  • Complex: Bacteriophage PR772

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Supramolecule #1: Bacteriophage PR772

SupramoleculeName: Bacteriophage PR772 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Wild type
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Molecular weightTheoretical: 100 KDa

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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

Concentration7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 3-40 / Number grids imaged: 1 / Number real images: 3200 / Average electron dose: 40.0 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: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 56000
CTF correctionSoftware - Name: RELION (ver. 3.0.7)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.0.7) / Number images used: 2784480
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.7)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.8.9.1)
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 104.93 / Target criteria: Cross-correlation coefficient

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