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- EMDB-0618: Icosahedral reconstruction of the thermophilic bacteriophage P74-... -

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Basic information

Database: EMDB / ID: EMD-0618
TitleIcosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid
Map data
SampleThermus phage P7426 (bacteriophage):
virus / Major head protein / P74-26 Head Decoration Protein
Function / homologyMajor capsid protein GpE / Uncharacterized protein / Major head protein
Function and homology information
Biological speciesThermus phage P7426 (bacteriophage) / Thermus virus P74-26 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsStone NP / Demo G / Agnello E / Kelch BA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nat Commun / Year: 2019
Title: Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure.
Authors: Nicholas P Stone / Gabriel Demo / Emily Agnello / Brian A Kelch /
Abstract: The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To ...The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.
Validation ReportPDB-ID: 6o3h

SummaryFull reportAbout validation report
DepositionFeb 26, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o3h
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6o3h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_0618.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 1024 pix.
= 1084.416 Å
1.06 Å/pix.
x 1024 pix.
= 1084.416 Å
1.06 Å/pix.
x 1024 pix.
= 1084.416 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Contour LevelBy AUTHOR: 12.5 / Movie #1: 12.5
Minimum - Maximum-7.5911107 - 32.043087
Average (Standard dev.)0.111731134 (±4.700796)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 1084.416 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1084.4161084.4161084.416
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-7.59132.0430.112

Supplemental data

Sample components

Entire Thermus phage P7426

EntireName: Thermus phage P7426 (bacteriophage) / Number of components: 3

Component #1: virus, Thermus phage P7426

VirusName: Thermus phage P7426 / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Thermus phage P7426 (bacteriophage)
Source (natural)Host Species: Thermus thermophilus (bacteria) / Host species strain: HB8
Shell #1Name of element: P74-26 capsid / Diameter: 824.0 Å / T number (triangulation number): 7

Component #2: protein, Major head protein

ProteinName: Major head protein / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 46.680754 kDa
SourceSpecies: Thermus virus P74-26 (bacteriophage)

Component #3: protein, P74-26 Head Decoration Protein

ProteinName: P74-26 Head Decoration Protein / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 16.37663 kDa
SourceSpecies: Thermus virus P74-26 (bacteriophage)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
Support film45 second glow discharge, negative polarity, 20 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 200.0 - 1200.0 nm
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 4611

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 23174
3D reconstructionSoftware: FREALIGN / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1Target criteria: Correlation Coefficient / Refinement space: REAL
Output model

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