[English] 日本語
Yorodumi
- EMDB-2133: The Structure of Lactococcal Phage TP901-1 by electron microscopy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2133
TitleThe Structure of Lactococcal Phage TP901-1 by electron microscopy: the capsid
Map dataIcosahedral reconstruction of the capsid of the phage TP901-1
Sample
  • Sample: Icosahedral capsid of the lactococcal phage TP901-1
  • Virus: Lactococcus phage TP901-1 (virus)
KeywordsEM / capsid / icosahedral / tp901 / lactococcal phage
Biological speciesLactococcus phage TP901-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsBebeacua C / Lai L / Skovgaard Vegge C / Brondsted L / van Heel M / Veesler D / Cambillau C
CitationJournal: J Virol / Year: 2013
Title: Visualizing a complete Siphoviridae member by single-particle electron microscopy: the structure of lactococcal phage TP901-1.
Authors: Cecilia Bebeacua / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Marin van Heel / David Veesler / Christian Cambillau /
Abstract: Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive ...Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium Lactococcus lactis using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection.
History
DepositionJun 11, 2012-
Header (metadata) releaseNov 21, 2012-
Map releaseNov 21, 2012-
UpdateJan 9, 2013-
Current statusJan 9, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2133.tif

Downloads & links

-
Map

FileDownload / File: emd_2133.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of the capsid of the phage TP901-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.2 Å/pix.
x 256 pix.
= 819.2 Å		3.2 Å/pix.
x 256 pix.
= 819.2 Å		3.2 Å/pix.
x 256 pix.
= 819.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-2.31868172 - 8.4837513
Average (Standard dev.)0.10018362 (±0.67388016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 819.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.23.23.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z819.200819.200819.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-2.3198.4840.100

-
Supplemental data

-
Sample components

-
Entire : Icosahedral capsid of the lactococcal phage TP901-1

EntireName: Icosahedral capsid of the lactococcal phage TP901-1
Components
  • Sample: Icosahedral capsid of the lactococcal phage TP901-1
  • Virus: Lactococcus phage TP901-1 (virus)

-
Supramolecule #1000: Icosahedral capsid of the lactococcal phage TP901-1

SupramoleculeName: Icosahedral capsid of the lactococcal phage TP901-1 / type: sample / ID: 1000
Details: The sample corresponded to the full phage but only the capsid particles were selected.
Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa

-
Supramolecule #1: Lactococcus phage TP901-1

SupramoleculeName: Lactococcus phage TP901-1 / type: virus / ID: 1
Details: The sample contained the full phages with tail and baseplate. Only the capsids were selected.
NCBI-ID: 35345 / Sci species name: Lactococcus phage TP901-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa
Virus shellShell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: SM buffer (100 mM sodium chloride, 10 mM magnesium sulfate, 50 mM Tris [pH 7.5], and 0.01% [wt/vol] gelatin)
GridDetails: Quantifoil grids were glow discharged for 20 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureMin: 80 K / Max: 105 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 130,000 times magnification.
Specialist opticsEnergy filter - Name: FEI
DateJun 1, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 200 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsThe particles were submitted to single-particle analysis with icosahedral symmetry using IMAGIC-V
CTF correctionDetails: Images
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 1500
Final angle assignmentDetails: ICOSAHEDRAL

-
Atomic model buiding 1

Initial modelPDB ID:

1ohg

SoftwareName: Chimera
DetailsProtocol: Rigid body. Manually fitted 60 copies of the hexamer of HK97. Every hexamer was refined using Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 10

+
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