[English] 日本語
Yorodumi
- PDB-6yeg: Hybrid structure of the SPP1 tail tube by solid-state NMR and cry... -

+
Open data


ID or keywords:

Loading...

-
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 / 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)
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, 1items
OrganizationGrant numberCountry
European Research Council (ERC)337490 Germany
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10792
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10792
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
  • Download structure data
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

-
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 (bacteriophage) / Gene: 17.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O48449

-
Experimental details

-
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

-
Sample preparation

ComponentName: SPP1 tail tube / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Bacillus phage SPP1 (bacteriophage)
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

-
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

-
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
Refinement-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

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more