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

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1996
TitleBubblegrams reveal the inner body of bacteriophage phiKZ
Keywordsinner body / core protein / asymmetric reconstruction / phiKZ / protein mapping
SamplephiKZ mature phage
SourcePseudomonas phage phiKZ / virus / phiKZ
Map dataThis is the inner body structure of bacteriophage phiKZ.
Methodsingle particle reconstruction, at 37 Å resolution
AuthorsWu W / Thomas JA / Cheng N / Black LW / Steven AC
CitationScience, 2012, 335, 182-182

Science, 2012, 335, 182-182 StrPapers
Bubblegrams reveal the inner body of bacteriophage φKZ.
Weimin Wu / Julie A Thomas / Naiqian Cheng / Lindsay W Black / Alasdair C Steven

DateDeposition: Nov 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Nov 23, 2011

Structure visualization

  • 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
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1996.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
10.03 Å/pix.
= 1604.16 Å
160 pix
10.03 Å/pix.
= 1604.16 Å
160 pix
10.03 Å/pix.
= 1604.16 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 10.026 Å
Contour Level:750 (by author), 750 (movie #1):
Minimum - Maximum-5409.6 - 9004.46
Average (Standard dev.)10.7033 (238.579)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1604.16 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-56-56-55
MAP C/R/S123
start NC/NR/NS-80-80-80
D min/max/mean-5409.5959004.45910.703

Supplemental data

Sample components

Entire phiKZ mature phage

EntireName: phiKZ mature phage / Number of components: 5
Oligomeric State: Inner body inside the capsid surrounding by DNA

Component #1: virus, Pseudomonas phage phiKZ

VirusName: Pseudomonas phage phiKZ / a.k.a: phiKZ / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Pseudomonas phage phiKZ / virus / phiKZ
Source (natural)Host Species: Pseudomonas aeruginosa / bacteria / シュードモナス・エルジノーサ, 緑膿菌

Experimental details

Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 40 %

Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jan 20, 2011
Details: Image 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.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 12 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 38000 X (nominal), 38000 X (calibrated) / Astigmatism: condenser and objective lens astigmatism / Cs: 2 mm / Imaging mode: OTHER / Defocus: 800 - 1500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 95 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2775 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection match / Software: EMAN / CTF correction: Micrograph
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.
Resolution: 37 Å / Resolution method: FSC 0.5

About Yorodumi


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

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more