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Bubblegrams reveal the inner body of bacteriophage phiKZ

by single particle reconstruction, at 37 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 750, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 750, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1996
TitleBubblegrams reveal the inner body of bacteriophage phiKZ
MapThis is the inner body structure of bacteriophage phiKZ.
SamplephiKZ mature phage
Keywordsinner body, core protein, asymmetric reconstruction, phiKZ, protein mapping
AuthorsWu W, Thomas JA, Cheng N, Black LW, Steven AC
DateDeposition: 2011-11-23, Header release: 2012-01-13, Map release: 2012-01-13, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 750, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 750, Image by UCSF CHIMERA

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Article
Citation - Primary
ArticleScience, Vol. 335, Issue 6065, Page 182, Year 2012
TitleBubblegrams reveal the inner body of bacteriophage φKZ.
AuthorsWeimin 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.
KeywordsCapsid (ultrastructure), Cryoelectron Microscopy, DNA, Viral, Image Processing, Computer-Assisted, Nucleocapsid (ultrastructure), Pseudomonas Phages (chemistry), Viral Proteins (analysis)
LinksDOI: 10.1126/science.1214120, PubMed: 22246767, PMC: PMC3462320
Map
Fileemd_1996.map.gz ( map file in CCP4 format, 16001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
10.026 A/pix
= 1604.16 A
160 pix
10.026 A/pix
= 1604.16 A
160 pix
10.026 A/pix
= 1604.16 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:750 (by author), 750 (movie #1):
Minimum - Maximum: -5409.6 - 9004.46
Average (Standard dev.): 10.7033 (238.579)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
Unit CellA= B= C: 1604.16 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 10.026 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5409.5959004.45910.703
Annotation DetailsThis is the inner body structure of bacteriophage phiKZ.
Supplement
Images
Images
Sample
NamephiKZ mature phage
Number of Components5
Oligomeric StateInner body inside the capsid surrounding by DNA
Component #1: virus - phiKZ
Scientific namePseudomonas phage phiKZ
Common NamephiKZ
Scientific Name of SpeciesPseudomonas phage phiKZ
Common Name of SpeciesphiKZ
NCBI taxonomy169683
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 287
Host Species: Pseudomonas aeruginosa
Host Category: BACTERIA(EUBACTERIA)
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
Humidity40
InstrumentNONE
Temperature100 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Date20-JAN-2011
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.
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose12 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 38000, Calibrated: 38000
Astigmatismcondenser and objective lens astigmatism
Nominal Cs2 mm
Imaging ModeOTHER
Defocus800 nm - 1500 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature100 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images95
Sampling Size6.35
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection match
SoftwareEMAN
CTF CorrectionMicrograph
DetailsProjection 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 Author37 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections2775
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1996.xml (7.1 KB)
Map dataemd_1996.map.gz (394.8 KB)
Images1996.png (141.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1996
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