[English] 日本語
Yorodumi
- EMDB-1996: Bubblegrams reveal the inner body of bacteriophage phiKZ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1996
TitleBubblegrams reveal the inner body of bacteriophage phiKZ
Map dataThis is the inner body structure of bacteriophage phiKZ.
Sample
  • Sample: phiKZ mature phage
  • Virus: Pseudomonas phage phiKZ (virus)
Keywordsinner body / core protein / asymmetric reconstruction / phiKZ / protein mapping
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 37.0 Å
AuthorsWu W / Thomas JA / Cheng N / Black LW / Steven AC
CitationJournal: Science / Year: 2012
Title: Bubblegrams reveal the inner body of bacteriophage φKZ.
Authors: Weimin Wu / Julie A Thomas / Naiqian Cheng / Lindsay W Black / Alasdair C Steven /
Abstract: Dense packing of macromolecules in cellular compartments and higher-order assemblies makes it difficult to pick out even quite large components in electron micrographs, despite nominally high ...Dense packing of macromolecules in cellular compartments and higher-order assemblies makes it difficult to pick out even quite large components in electron micrographs, despite nominally high resolution. Immunogold labeling and histochemical procedures offer ways to map certain components but are limited in their applicability. Here, we present a differential mapping procedure, based on the physical principle of protein's greater sensitivity to radiation damage compared with that of nucleic acid.
History
DepositionNov 23, 2011-
Header (metadata) releaseJan 13, 2012-
Map releaseJan 13, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 750
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 750
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1996.png

Downloads & links

-
Map

FileDownload / File: emd_1996.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the inner body structure of bacteriophage phiKZ.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.03 Å/pix.
x 160 pix.
= 1604.16 Å		10.03 Å/pix.
x 160 pix.
= 1604.16 Å		10.03 Å/pix.
x 160 pix.
= 1604.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.026 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 750.0 / Movie #1: 750
Minimum - Maximum-5409.600000000000364 - 9004.459999999999127
Average (Standard dev.)10.7033 (±238.579000000000008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 1604.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.02610.02610.026
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z1604.1601604.1601604.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-5409.5959004.45910.703

-
Supplemental data

-
Sample components

-
Entire : phiKZ mature phage

EntireName: phiKZ mature phage
Components
  • Sample: phiKZ mature phage
  • Virus: Pseudomonas phage phiKZ (virus)

-
Supramolecule #1000: phiKZ mature phage

SupramoleculeName: phiKZ mature phage / type: sample / ID: 1000
Oligomeric state: Inner body inside the capsid surrounding by DNA
Number unique components: 5

-
Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Name.synonym: phiKZ / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: phiKZ
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / synonym: BACTERIA(EUBACTERIA)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 100 K / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: condenser and objective lens astigmatism
DetailsImage pairs. First low dose image, 12 electrons per angstrom squared, then high dose to get radiation damage (same dose but longer time), dose about 5-fold of low dose.
DateJan 20, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 95 / Average electron dose: 12 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: Micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Projection match method was used to determine the unique vertex and the orientation of tail. The inner body was solved directly from 2D data without using any initial model.
Number images used: 2775

+
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