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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
Sample
  • Complex: SPP1 tail tube
    • Protein or peptide: Tail tube protein gp17.1*
Keywordscomplex / tail tube / scaffolding / DNA transport / VIRAL PROTEIN
Function / homology
Function and homology information


viral head-tail joining / virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism
Similarity search - Function
Phage major tail protein TP901-1 / Phage tail tube protein / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tail tube protein gp17.1*
Similarity search - Component
Biological speciesBacillus phage SPP1 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZinke M / Sachowsky KAA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)337490European Union
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
History
DepositionMar 24, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing 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
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  • 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
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  • 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10792.png

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)
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

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10792_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SPP1 tail tube

EntireName: SPP1 tail tube
Components
  • Complex: SPP1 tail tube
    • Protein or peptide: Tail tube protein gp17.1*

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Supramolecule #1: SPP1 tail tube

SupramoleculeName: SPP1 tail tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus phage SPP1 (virus)

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Macromolecule #1: Tail tube protein gp17.1*

MacromoleculeName: Tail tube protein gp17.1* / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPP1 (virus)
Molecular weightTheoretical: 19.674451 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPIMGQDVKY LFQSIDAATG SAPLFPAYQT DGSVSGEREL FDEQTKNGRI LGPGSVADSG EVTYYGKRGD AGQKAIEDAY QNGKQIKFW RVDTVKNEND KYDAQFGFAY IESREYSDGV EGAVEISISL QVIGELKNGE IDTLPEEIVN VSKGGYDFQQ P GQTTGEAP GTVPAPHHHH HH

UniProtKB: Tail tube protein gp17.1*

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
0.5 MNaClSodium chloridesodium chloride
1.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 3.0 sec. / Average electron dose: 70.0 e/Å2
Details: 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 .
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: C6 symmetry and rough estimate of the helical symmetry (rise of 40 A and a twist of 21 deg) was used for initial reconstructions. In the initial model spheres were placed at positions given by the symmetry.
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 38.46 Å
Applied symmetry - Helical parameters - Δ&Phi: 21.89 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 5966
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6yeg:
Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement

PDB-6yq5:
Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - NMR Ensemble

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