[English] 日本語
Yorodumi
- PDB-5li2: bacteriophage phi812K1-420 tail sheath and tail tube protein in n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5li2
Titlebacteriophage phi812K1-420 tail sheath and tail tube protein in native tail
Components
  • Phage-like element PBSX protein XkdM
  • tail sheath protein
KeywordsVIRAL PROTEIN / polyvalent staphylococcal bactoriophage / Myoviridae / tail sheath / tail contraction
Function / homologyPhage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Major tail sheath protein / Phage-like element PBSX protein XkdM
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Staphylococcus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsNovacek, J. / Siborova, M. / Benesik, M. / Pantucek, R. / Doskar, J. / Plevka, P.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLQ1601 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2010005 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2011033 Czech Republic
Grant Agency of the Czech Republic15-21631Y Czech Republic
European Molecular Biology Organization3041 Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate.
Authors: Jiří Nováček / Marta Šiborová / Martin Benešík / Roman Pantůček / Jiří Doškař / Pavel Plevka /
Abstract: Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall ...Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall and serve as a channel for the transport of the phage genome into the cytoplasm. However, the mechanisms controlling the tail contraction and genome release of phages with "double-layered" baseplates were unknown. We used cryo-electron microscopy to show that the binding of the Twort-like phage phi812 to the Staphylococcus aureus cell wall requires a 210° rotation of the heterohexameric receptor-binding and tripod protein complexes within its baseplate about an axis perpendicular to the sixfold axis of the tail. This rotation reorients the receptor-binding proteins to point away from the phage head, and also results in disruption of the interaction of the tripod proteins with the tail sheath, hence triggering its contraction. However, the tail sheath contraction of Myoviridae phages is not sufficient to induce genome ejection. We show that the end of the phi812 double-stranded DNA genome is bound to one protein subunit from a connector complex that also forms an interface between the phage head and tail. The tail sheath contraction induces conformational changes of the neck and connector that result in disruption of the DNA binding. The genome penetrates into the neck, but is stopped at a bottleneck before the tail tube. A subsequent structural change of the tail tube induced by its interaction with the S. aureus cell is required for the genome's release.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 3, 2018Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: em_software / pdbx_audit_support ...em_software / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Sep 16, 2020Group: Advisory / Category: pdbx_database_PDB_obs_spr

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4051
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4051
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tail sheath protein
B: tail sheath protein
C: tail sheath protein
D: tail sheath protein
E: tail sheath protein
F: tail sheath protein
G: Phage-like element PBSX protein XkdM
H: Phage-like element PBSX protein XkdM
I: Phage-like element PBSX protein XkdM
J: Phage-like element PBSX protein XkdM
K: Phage-like element PBSX protein XkdM
L: Phage-like element PBSX protein XkdM


Theoretical massNumber of molelcules
Total (without water)492,02712
Polymers492,02712
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15340 Å2
ΔGint-24 kcal/mol
Surface area180340 Å2
MethodPISA

-
Components

#1: Protein
tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus) / Gene: 812a_103, 812F1_103, K1/420_103, K1_103 / Production host: Staphylococcaceae (Staphylococcus group) / References: UniProt: A0A0U1WZ79
#2: Protein
Phage-like element PBSX protein XkdM


Mass: 17445.471 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus (bacteria) / Gene: xkdM, BSU12660 / Production host: Escherichia coli (E. coli) / References: UniProt: P54332

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Staphylococcus phage 812 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K420
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus
Virus shellDiameter: 1100 nm / Triangulation number (T number): 16
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisTrisHCl1
210 mMsodium chlorideNaClSodium chloride1
310 mMcalcium chlorideCaCl21
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.86 sec. / Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
5SPIDERCTF correction
11SPIDERinitial Euler assignment
12SPIDERfinal Euler assignment
13IHRSRfinal Euler assignment
14RELIONclassification
15SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 21.4 ° / Axial rise/subunit: 38.9 Å / Axial symmetry: C6
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3628 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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