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

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Basic information

Entry
Database: PDB / ID: 6yeg
TitleHybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement
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
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 supportEuropean Union, 1items
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, K.A.A. / Oster, C. / Zinn-Justin, S. / Ravelli, R. / Schroder, G.F. / Habeck, M. / Lange, A.
History
DepositionMar 24, 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 1.3Sep 13, 2023Group: Author supporting evidence / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_audit_support
Item: _pdbx_audit_support.country

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Structure visualization

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Structure viewerMolecule:
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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)236,09312
Polymers236,09312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51990 Å2
ΔGint-171 kcal/mol
Surface area90990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1all calculated structures submitted
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: 19674.451 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
1154anisotropic13D HNhH
1145anisotropic13D HNhH
1136anisotropic13D HNhH
1127anisotropic13D HNhH
1168anisotropic13D HNhH
1179anisotropic13D HNhH
11810anisotropic13D HNhH

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Sample preparation

ComponentName: SPP1 tail tube / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus phage SPP1 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTRISC4H11NO31
20.5 Msodium chlorideNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acidC10H16N2O81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Details
TypeSolution-IDContentsLabelSolvent system
fiber1100 % u-2H13C15N; 100% back-exchange gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, soliduniformsolid
fiber2100 % isoleucine-(1HD1, 13CD1)-u-15N; 100% back-exchange gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidisoleucine-methylsolid
fiber3100 % 50% isoleucine-(1HD1, 13CD1)-u-14N & 50% u-15N; 100% back-exchange gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidisoleucine-methyl mixsolid
fiber4100 % alanine-(1HB, 13CB)-u-15N; 100% back-exchange 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% back-exchanged 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% back-exchanged 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% back-exchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidLV-methyl mixsolid
fiber8100 % threonine-(1HG2, 13CG2)-u-15N; 100% back-exchanged 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% back-exchanged gp17.1, 20 mM sodium phosphate, 500 mM sodium chloride, 1 mM EDTA, solidthreonine-methyl mixsolid
fiber10100 % methionine-(1HE, 13CE)-u-15N; 100% back-exchanged 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% back-exchanged 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% back-exchange1
20 mMsodium phosphatenatural abundance1
500 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
100 %gp17.1isoleucine-(1HD1, 13CD1)-u-15N; 100% back-exchange2
20 mMsodium phosphatenatural abundance2
500 mMsodium chloridenatural abundance2
1 mMEDTAnatural abundance2
100 %gp17.150% isoleucine-(1HD1, 13CD1)-u-14N & 50% u-15N; 100% back-exchange3
20 mMsodium phosphatenatural abundance3
500 mMsodium chloridenatural abundance3
1 mMEDTAnatural abundance3
100 %gp17.1alanine-(1HB, 13CB)-u-15N; 100% back-exchange4
20 mMsodium phosphatenatural abundance4
500 mMsodium chloridenatural abundance4
1 mMEDTAnatural abundance4
100 %gp17.150% alanine-(1HB, 13CB)-u-14N & 50% u-15N; 100% back-exchanged5
20 mMsodium phosphatenatural abundance5
500 mMsodium chloridenatural abundance5
1 mMEDTAnatural abundance5
100 %gp17.1leucine-(1HD, 13CD)proR-valine-(1HG, 13CG)proR-u-15N; 100% back-exchanged6
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% back-exchanged7
20 mMsodium phosphatenatural abundance7
500 mMsodium chloridenatural abundance7
1 mMEDTAnatural abundance7
100 %gp17.1threonine-(1HG2, 13CG2)-u-15N; 100% back-exchanged8
20 mMsodium phosphatenatural abundance8
500 mMsodium chloridenatural abundance8
1 mMEDTAnatural abundance8
100 %gp17.150% threonine-(1HG2, 13CG2)-u-14N & 50% u-15N; 100% back-exchanged9
20 mMsodium phosphatenatural abundance9
500 mMsodium chloridenatural abundance9
1 mMEDTAnatural abundance9
100 %gp17.1methionine-(1HE, 13CE)-u-15N; 100% back-exchanged10
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% back-exchanged11
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 FIELDBright-field microscopy
Image recordingAverage exposure time: 3 sec. / Electron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
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

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.3image acquisition
4Gctf1.06CTF correction
12RELION2.13D reconstruction
13PHENIX1.11.1model refinement
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: 5966 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616200
ELECTRON MICROSCOPYf_angle_d1.03121732
ELECTRON MICROSCOPYf_dihedral_angle_d8.6269528
ELECTRON MICROSCOPYf_chiral_restr0.0542268
ELECTRON MICROSCOPYf_plane_restr0.0062964
NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
Inferential Structure Determination (ISD)Rieping, Nilges, Habeckstructure calculation
RefinementMethod: na / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

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