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- EMDB-10792: Hybrid structure of the SPP1 tail tube by solid-state NMR and cry... -

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Basic information

Entry
Database: EMDB / ID: EMD-10792
TitleHybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement
Map data
SampleSPP1 tail tube:
Tail tube protein gp17.1*
Function / homologyFibronectin type III / Phage major tail protein TP901-1 / Immunoglobulin-like fold / Fibronectin type III superfamily / viral head-tail joining / viral genome ejection through host cell envelope, long flexible tail mechanism / virus tail, tube / virion / Tail tube protein gp17.1*
Function and homology information
Biological speciesBacillus phage SPP1 (bacteriophage)
Methodhelical reconstruction / cryo EM / Resolution: 4 Å
AuthorsZinke M / Sachowsky KAA / Zinn-Justin S / Ravelli R / Schroder GF / Habeck M / Lange A
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)337490 Germany
Citation
Journal: Nat Commun / Year: 2020
Title: Architecture of the flexible tail tube of bacteriophage SPP1.
Authors: Maximilian Zinke / Katrin A A Sachowsky / Carl Öster / Sophie Zinn-Justin / Raimond Ravelli / Gunnar F Schröder / Michael Habeck / Adam Lange /
Abstract: Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that ...Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.
#1: Journal: Biorxiv / Year: 2020
Title: Spinal Column Architecture of the Flexible SPP1 Bacteriophage Tail Tube
Authors: Zinke M / Sachowsky KAA / Oster C / Zinn-Justin S / Ravelli R / Schroder GF / Habeck M / Lange A
Validation ReportPDB-ID: 6yeg

SummaryFull report
PDB-ID: 6yq5

SummaryFull report
About validation report
History
DepositionMar 24, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.27
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yeg
  • Surface level: 1.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yq5
  • Surface level: 1.27
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yeg
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yq5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10792.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 200 pix.
= 187. Å
0.94 Å/pix.
x 200 pix.
= 187. Å
0.94 Å/pix.
x 200 pix.
= 187. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density
Contour LevelBy AUTHOR: 1.27 / Movie #1: 1.27
Minimum - Maximum-4.415271 - 2.4558156
Average (Standard dev.)0.07454041 (±0.38211346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 187.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9350.9350.935
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z187.000187.000187.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-4.4152.4560.075

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Supplemental data

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Half map: #1

Fileemd_10792_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10792_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SPP1 tail tube

EntireName: SPP1 tail tube / Number of components: 2

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Component #1: protein, SPP1 tail tube

ProteinName: SPP1 tail tube / Recombinant expression: No
SourceSpecies: Bacillus phage SPP1 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #2: protein, Tail tube protein gp17.1*

ProteinName: Tail tube protein gp17.1* / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 19.674451 kDa
SourceSpecies: Bacillus phage SPP1 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C6 (6 fold cyclic) / Delta z: 38.46 Å / Delta phi: 21.89 %deg;
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 70 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionDetails: Images were collected in movie-mode at 20 fractions, each fraction had 6 frames. Dose rate was 23 e/A^2/s, i.e. dose per frame was 3.5 electrons/A^2 .

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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