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- PDB-6yq5: Hybrid structure of the SPP1 tail tube by solid-state NMR and cry... -

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Basic information

Entry
Database: PDB / ID: 6yq5
TitleHybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - NMR Ensemble
ComponentsTail tube protein gp17.1*
KeywordsVIRAL PROTEIN / complex / tail tube / scaffolding / DNA transport
Function / homology
Function and homology information


viral head-tail joining / virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral translational frameshifting
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)
MethodELECTRON MICROSCOPY / SOLID-STATE NMR / helical reconstruction / na / cryo EM / Resolution: 4 Å
AuthorsZinke, M. / Sachowsky, K.A.A. / Zinn-Justin, S. / Ravelli, R. / Schroder, G.F. / Habeck, M. / Lange, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 860 TP B09 Germany
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, K.A.A. / Oster, C. / Zinn-Justin, S. / Ravelli, R. / Schroder, G.F. / Habeck, M. / Lange, A.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jul 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Assembly

Deposited unit
A: Tail tube protein gp17.1*
B: Tail tube protein gp17.1*
C: Tail tube protein gp17.1*
D: Tail tube protein gp17.1*
E: Tail tube protein gp17.1*
F: Tail tube protein gp17.1*
G: Tail tube protein gp17.1*
H: Tail tube protein gp17.1*
I: Tail tube protein gp17.1*
J: Tail tube protein gp17.1*
K: Tail tube protein gp17.1*
L: Tail tube protein gp17.1*


Theoretical massNumber of molelcules
Total (without water)223,40712
Polymers223,40712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area49010 Å2
ΔGint-137 kcal/mol
Surface area87450 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500target function
RepresentativeModel #1target function

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Components

#1: Protein
Tail tube protein gp17.1* / TTP / Gene product 17.1 / gp17.1 / Major tail protein / MTP


Mass: 18617.258 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPP1 (virus) / Gene: 17.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O48449

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Experimental details

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Experiment

Experiment
Method
ELECTRON MICROSCOPY
SOLID-STATE NMR
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic14D HNhhNH
122anisotropic13D HChH
136anisotropic13D HChH
142anisotropic12D hCH
154anisotropic12D hCH
166anisotropic12D hCH
178anisotropic12D hCH
1810anisotropic12D hCH
1911anisotropic12D hCH
1102anisotropic13D HNhH
1113anisotropic13D HNhH
1124anisotropic13D HNhH
1135anisotropic13D HNhH
1186anisotropic13D HNhH
1177anisotropic13D HNhH
1168anisotropic13D HNhH
1149anisotropic13D HNhH
11510anisotropic13D HNhH

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Sample preparation

ComponentName: helical arrangement of hexameric rings of gp17.1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus phage SPP1 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusType: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTRISC4H11NO31
2200 mMsodium chlorideNaCl1
31 mMEDTAC10H16N2O81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Details
TypeSolution-IDContentsLabelSolvent system
fiber1100 % u-2H13C15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, soliduniformsolid
fiber2100 % isoleucine-(1HD1, 13CD1)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidisoleucin-methylsolid
fiber3100 % 50% isoleucine-(1HD1, 13CD1)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidisoleucin-methyl mixsolid
fiber4100 % alanine-(1HB, 13CB)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidalanine-methylsolid
fiber5100 % 50% alanine-(1HB, 13CB)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidalanine-methyl mixsolid
fiber6100 % leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidLV-methylsolid
fiber7100 % 50% leucine-(1HD, 13CD)proR- valine-(1HG, 13CG)proR-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidLV-methyl mixsolid
fiber8100 % threonine-(1HG2, 13CG2)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidthreonine-methylsolid
fiber9100 % 50% threonine-(1HG2, 13CG2)-u-14N & 50% u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidthreonine-methyl mixsolid
fiber10100 % methionine-(1HE, 13CE)-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidmethionine-methylsolid
fiber11100 % alanine-(1HB, 13CB)- isoleucine-(1HD1, 13CD1)-( 1HG2, 13CG2)-leucine-(1HD, 13CD)proR/proS-valine-(1HG, 13CG)proR/proS-u-15N; 100% backexchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidassignmentsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 %gp17.1u-2H13C15N; 100% backexchanged1
20 mMsodium phosphatenatural abundance1
500 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
100 %gp17.1isoleucine-(1HD1, 13CD1)-u-15N; 100% backexchanged2
20 mMsodium phosphatenatural abundance2
500 mMsodium chloridenatural abundance2
1 mMEDTAnatural abundance2
100 %gp17.150% isoleucine-(1HD1, 13CD1)-u-14N & 50% u-15N; 100% backexchanged3
20 mMsodium phosphatenatural abundance3
500 mMsodium chloridenatural abundance3
1 mMEDTAnatural abundance3
100 %gp17.1alanine-(1HB, 13CB)-u-15N; 100% backexchanged4
20 mMsodium phosphatenatural abundance4
500 mMsodium chloridenatural abundance4
1 mMEDTAnatural abundance4
100 %gp17.150% alanine-(1HB, 13CB)-u-14N & 50% u-15N; 100% backexchanged5
20 mMsodium phosphatenatural abundance5
500 mMsodium chloridenatural abundance5
1 mMEDTAnatural abundance5
100 %gp17.1leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% backexchanged6
20 mMsodium phosphatenatural abundance6
500 mMsodium chloridenatural abundance6
1 mMEDTAnatural abundance6
100 %gp17.150% leucine-(1HD, 13CD)proR- valine-(1HG, 13CG)proR-u-14N & 50% u-15N; 100% backexchanged7
20 mMsodium phosphatenatural abundance7
500 mMsodium chloridenatural abundance7
1 mMEDTAnatural abundance7
100 %gp17.1threonine-(1HG2, 13CG2)-u-15N; 100% backexchanged8
20 mMsodium phosphatenatural abundance8
500 mMsodium chloridenatural abundance8
1 mMEDTAnatural abundance8
100 %gp17.150% threonine-(1HG2, 13CG2)-u-14N & 50% u-15N; 100% backexchanged9
20 mMsodium phosphatenatural abundance9
500 mMsodium chloridenatural abundance9
1 mMEDTAnatural abundance9
100 %gp17.1methionine-(1HE, 13CE)-u-15N; 100% backexchanged10
20 mMsodium phosphatenatural abundance10
500 mMsodium chloridenatural abundance10
1 mMEDTAnatural abundance10
100 %gp17.1alanine-(1HB, 13CB)- isoleucine-(1HD1, 13CD1)-( 1HG2, 13CG2)-leucine-(1HD, 13CD)proR/proS-valine-(1HG, 13CG)proR/proS-u-15N; 100% backexchanged11
20 mMsodium phosphatenatural abundance11
500 mMsodium chloridenatural abundance11
1 mMEDTAnatural abundance11
Sample conditionsIonic strength: 0.5 M / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 291 K

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 3 sec. / Electron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 853
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 .
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 21.89 ° / Axial rise/subunit: 38.46 Å / Axial symmetry: C6
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5965 / Symmetry type: HELICAL
NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
Inferential Structure Determination (ISD)Rieping, Nilges, Habeckstructure calculation
RefinementMethod: na / Software ordinal: 6
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 10

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