[English] 日本語
- EMDB-5383: Marine Bacteriophage SIO-2 with T12 symmetry (Procapsid) -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 5383
TitleMarine Bacteriophage SIO-2 with T12 symmetry (Procapsid)
Keywordsprocapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like
SampleMarine Phage SIO-2
SourceVibrio phage SIO-2 / virus / SIO-2
Map dataSIO-2 prophage
Methodsingle particle (icosahedral) reconstruction, at 15 Å resolution
AuthorsLander GC / Baudoux AC / Azam F / Potter CS / Carragher B / Johnson JE
CitationStructure, 2012, 20, 498-503

Structure, 2012, 20, 498-503 Yorodumi Papers
Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM.
Gabriel C Lander / Anne-Claire Baudoux / Farooq Azam / Clinton S Potter / Bridget Carragher / John E Johnson

DateDeposition: Jan 10, 2012 / Header (metadata) release: Jan 12, 2012 / Map release: Jan 12, 2012 / Last update: Mar 14, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5383.map.gz (map file in CCP4 format, 22783 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
3.9 Å/pix.
= 702. Å
180 pix
3.9 Å/pix.
= 702. Å
180 pix
3.9 Å/pix.
= 702. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.9 Å
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-6.16991615 - 13.7131815
Average (Standard dev.)0.19893758 (1.02901757)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 702 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.93.93.9
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z702.000702.000702.000
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS101010
D min/max/mean-6.17013.7130.199

Supplemental data

Sample components

Entire Marine Phage SIO-2

EntireName: Marine Phage SIO-2 / Details: procapsid / Number of components: 1 / Oligomeric State: immature capsid
MassTheoretical: 12.2 MDa

Component #1: virus, Vibrio phage SIO-2

VirusName: Vibrio phage SIO-2 / a.k.a: SIO-2 / Class: VIRION / Details: particles were present with mature phage prep / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 12.2 MDa
SpeciesSpecies: Vibrio phage SIO-2 / virus / SIO-2
Source (natural)Host Species: Vibrio sp. swat-3 / bacteria / Host category: BACTERIA(EUBACTERIA)
Shell #1Name of element: gene84 / Diameter: 600 Å / T number(triangulation number): 12

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 100 kDa-filtered autoclaved seawater
Support film200 mesh Cu grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 78 K / Humidity: 100 % / Method: blot for 4 seconds before plunging / Details: Vitrification instrument: Vitrobot

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Jun 13, 2009 / Details: Collected using Leginon software
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 80000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 210K times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 3000 nm
Specimen HolderHolder: Gatan CT3500 / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 6628 / Sampling size: 0.975 microns

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: particles automatically selected and manually edited
Number of projections: 1179 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection matching / Software: EMAN and Frealign / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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)

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