EMDB-1996: Bubblegrams reveal the inner body of bacteriophage phiKZ

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1996
Title	Bubblegrams reveal the inner body of bacteriophage phiKZ
Map	This is the inner body structure of bacteriophage phiKZ.
Sample	phiKZ mature phage
Keywords	inner body, core protein, asymmetric reconstruction, phiKZ, protein mapping
Authors	Wu W, Thomas JA, Cheng N, Black LW, Steven AC
Date	Deposition: 2011-11-23, Header release: 2012-01-13, Map release: 2012-01-13, Last update: 2012-09-26
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 750, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 750, Made by UCSF CHIMERA
Supplemental images	1996.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-5409 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Science, Vol. 335, Issue 6065, Page 182, 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 Laboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA.
Keywords	Capsid (ultrastructure), Cryoelectron Microscopy, DNA, Viral, Image Processing, Computer-Assisted, Nucleocapsid (ultrastructure), Pseudomonas Phages (chemistry), Viral Proteins (analysis)
Links	DOI: 10.1126/science.1214120, PubMed: 22246767, PMC: PMC3462320

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 1604.16 A , B = 1604.16 A , C = 1604.16 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 10.026 A , Y = 10.026 A , Z = 10.026 A

CCP4 map header info

Annotation Details

This is the inner body structure of bacteriophage phiKZ.

Sample
Name	phiKZ mature phage
Number of Components	5
Oligomeric State	Inner body inside the capsid surrounding by DNA
Component #1: virus - phiKZ
Scientific name	Pseudomonas phage phiKZ
Common Name	phiKZ
Scientific Name of Species	Pseudomonas phage phiKZ (NCBI Taxonomy: 169683)
Common Name of Species	phiKZ
Empty	No
Enveloped	No
Isolate	STRAIN
Class	VIRION
Natural Source	Host Species: Pseudomonas aeruginosa (NCBI Taxonomy: 287) Host Category: BACTERIA(EUBACTERIA)

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Humidity	40
Instrument	NONE
Temperature	100 Kelvin
Imaging
Microscope	FEI/PHILIPS CM200FEG
Date	20-JAN-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 Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	120 kV
Electron Dose	12 e/A**2
Illumination Mode	SPOT SCAN
Lens
Magnification	Nominal: 38000 X, Calibrated: 38000 X
Astigmatism	condenser and objective lens astigmatism
Nominal Cs	2.0 mm
Imaging Mode	OTHER
Defocus	800 nm - 1500 nm
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Temperature	100 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	NIKON SUPER COOLSCAN 9000
Number of Digital Images	95
Sampling Size	6.35 microns
Quant Bit Number	16

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	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 By Author	37
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	2775

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 5.2 MB Session file for UCSF-Chimera, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.8 MB Session file for UCSF-Chimera, 26.5 KB