[English] 日本語
Yorodumi
- EMDB-2340: The electron microscopy reconstruction of the baseplate of lactoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2340
TitleThe electron microscopy reconstruction of the baseplate of lactococcal phage Tuc2009.
Map dataReconstruction of the baseplate of lactococcal phage Tuc2009
Sample
  • Sample: Baseplate of lactoccocal phage Tuc2009
  • Virus: Lactococcus phage Tuc2009 (virus)
Keywordslactococcal phage / tuc2009 / baseplate / electron microscopy / single-particle
Biological speciesLactococcus phage Tuc2009 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 36.0 Å
AuthorsCollins B / Bebeacua C / Mahony J / Douillard F / Veesler D / Blangy B / Cambillau C / van Sinderen D
CitationJournal: J Virol / Year: 2013
Title: Structure and functional analysis of the host recognition device of lactococcal phage tuc2009.
Authors: Barry Collins / Cecilia Bebeacua / Jennifer Mahony / Stéphanie Blangy / François P Douillard / David Veesler / Christian Cambillau / Douwe van Sinderen /
Abstract: Many phages employ a large heteropolymeric organelle located at the tip of the tail, termed the baseplate, for host recognition. Contrast electron microscopy (EM) of the lactococcal phage Tuc2009 ...Many phages employ a large heteropolymeric organelle located at the tip of the tail, termed the baseplate, for host recognition. Contrast electron microscopy (EM) of the lactococcal phage Tuc2009 baseplate and its host-binding subunits, the so-called tripods, allowed us to obtain a low-resolution structural image of this organelle. Structural comparisons between the baseplate of the related phage TP901-1 and that of Tuc2009 demonstrated that they are highly similar, except for the presence of an additional protein in the Tuc2009 baseplate (BppATuc2009), which is attached to the top of the Tuc2009 tripod structure. Recombinantly produced Tuc2009 or TP901-1 tripods were shown to bind specifically to their particular host cell surfaces and are capable of almost fully and specifically eliminating Tuc2009 or TP901-1 phage adsorption, respectively. In the case of Tuc2009, such adsorption-blocking ability was reduced in tripods that lacked BppATuc2009, indicating that this protein increases the binding specificity and/or affinity of the Tuc2009 tripod to its host receptor.
History
DepositionMar 27, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseJun 12, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.001
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.001
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2340.png

Downloads & links

-
Map

FileDownload / File: emd_2340.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the baseplate of lactococcal phage Tuc2009
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.95 Å/pix.
x 144 pix.
= 712.8 Å		4.95 Å/pix.
x 144 pix.
= 712.8 Å		4.95 Å/pix.
x 144 pix.
= 712.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001 / Movie #1: 0.001
Minimum - Maximum-0.0000302 - 0.04787388
Average (Standard dev.)0.00086621 (±0.00411965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 712.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.954.954.95
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z712.800712.800712.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.0000.0480.001

-
Supplemental data

-
Sample components

-
Entire : Baseplate of lactoccocal phage Tuc2009

EntireName: Baseplate of lactoccocal phage Tuc2009
Components
  • Sample: Baseplate of lactoccocal phage Tuc2009
  • Virus: Lactococcus phage Tuc2009 (virus)

-
Supramolecule #1000: Baseplate of lactoccocal phage Tuc2009

SupramoleculeName: Baseplate of lactoccocal phage Tuc2009 / type: sample / ID: 1000
Details: The baseplate was selected from images collected from a sample of the entire phages.
Oligomeric state: 6 / Number unique components: 1

-
Supramolecule #1: Lactococcus phage Tuc2009

SupramoleculeName: Lactococcus phage Tuc2009 / type: virus / ID: 1 / Name.synonym: Tuc2009 / NCBI-ID: 35241 / Sci species name: Lactococcus phage Tuc2009 / Virus type: OTHER / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Tuc2009
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / Strain: UC509.9 / synonym: BACTERIA(EUBACTERIA)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris-HCL, 10 mM MgSO4, 100 mM NaCl
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 20 seconds
GridDetails: 300 mesh copper grid with thin carbon layer, glow discharged for 30 seconds
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI 12
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateJun 1, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 2000 / Average electron dose: 10 e/Å2 / Details: Images were collected using a 2kx2k CCD camera
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 48500
Sample stageSpecimen holder: Room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC

-
Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Spider, Xmipp / Number images used: 2000

-
Atomic model buiding 1

Initial modelPDB ID:

4div
PDB Unreleased entry

SoftwareName: Chimera
DetailsThe baseplate was manually fitted and then automatically refined
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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