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- EMDB-8868: Structure of the tail spike of the marine siphovirus TW1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8868
TitleStructure of the tail spike of the marine siphovirus TW1
Map dataMarine Siphovirus TW1 Tail Spike
Sample
  • Virus: Pseudoalteromonas phage TW1 (virus)
Biological speciesPseudoalteromonas phage TW1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsWang Z / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1515260 United States
CitationJournal: Structure / Year: 2018
Title: Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes.
Authors: Zhiqing Wang / Stephen C Hardies / Andrei Fokine / Thomas Klose / Wen Jiang / Byung Cheol Cho / Michael G Rossmann /
Abstract: Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of ...Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of most of these proteins have been predicted by bioinformatic methods. A 3.6 Å resolution cryoelectron microscopy map of the icosahedrally averaged TW1 head showed the atomic structures of the major capsid protein, gp57, and the capsid-stabilizing protein, gp56. The gp57 structure is similar to that of the phage HK97 capsid protein. The gp56 protein has two domains, each having folds similar to that of the N-terminal part of phage λ gpD, indicating a common ancestry. The first gp56 domain clamps adjacent capsomers together, whereas the second domain is required for trimerization. A 6-fold-averaged reconstruction of the distal part of the tail showed that TW1 has six tail spikes, which are unusual for siphophages but are similar to the podophages P22 and Sf6, suggesting a common evolutionary origin of these spikes.
History
DepositionAug 1, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseJun 13, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8868_1.png

emd_8868_2.png

emd_8868_3.png

Downloads & links

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Map

FileDownload / File: emd_8868.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMarine Siphovirus TW1 Tail Spike
Voxel sizeX=Y=Z: 4.9 Å
Density
Contour LevelBy AUTHOR: 6.5 / Movie #1: 6.5
Minimum - Maximum-28.286041 - 25.750347
Average (Standard dev.)0.066257656 (±2.5606706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.94.94.9
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z588.000588.000588.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-28.28625.7500.066

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Supplemental data

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Sample components

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Entire : Pseudoalteromonas phage TW1

EntireName: Pseudoalteromonas phage TW1 (virus)
Components
  • Virus: Pseudoalteromonas phage TW1 (virus)

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Supramolecule #1: Pseudoalteromonas phage TW1

SupramoleculeName: Pseudoalteromonas phage TW1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 1366055 / Sci species name: Pseudoalteromonas phage TW1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudoalteromonas phenolica (bacteria)
Virus shellShell ID: 1 / Diameter: 620.0 Å / 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 - Name: SM buffer / Details: Tris 50mM pH7.5 NaCl 100mM MgSO4 8mM
GridModel: Quantifoil R2/1 / Mesh: 200 / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: OTHER / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2254
CTF correctionSoftware - Name: jspr (ver. ctfit2)
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 956

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