3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-2052

Capsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly

by single particle (icosahedral) reconstruction, at 10.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 8, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2052
TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
MapReconstruction of an SPP1 capsid after DNA ejection
SampleCapsid of SPP1
KeywordsBacteriophage Capsid SPP1
AuthorsWhite HE, Sherman MB, Brasiles S, Jacquet E, Seavers P, Tavares P, Orlova EV
DateDeposition: 2012-03-14, Header release: 2012-03-23, Map release: 2012-06-14, Last update: 2012-06-14
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 8, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Virol., Vol. 86, Issue 12, Page 6768-77, Year 2012
TitleCapsid structure and its stability at the late stages of bacteriophage SPP1 assembly.
AuthorsHelen E White, Michael B Sherman, Sandrine Brasilès, Eric Jacquet, Philippa Seavers, Paulo Tavares, Elena V Orlova
Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom.
KeywordsBacteriophages (chemistry), Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, Models, Molecular, Protein Stability, Virus Assembly
LinksDOI: 10.1128/JVI.00412-12, PubMed: 22514336, PMC: PMC3393595
Map
Fileemd_2052.map.gz ( map file in CCP4 format, 524289 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.49 A/pix
= 894. A
512 pix
1.49 A/pix
= 894. A
512 pix
1.491 A/pix
= 894.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Density
Contour Level:10 (by author), 8 (movie #1):
Minimum - Maximum: -22.61455727 - 34.57154846
Average (Standard dev.): 2E-8 (3.00000048)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin-255-256-256
Limit256255255
Spacing600600600
Unit CellA: 894.60004 A, B: 894 A, C: 894 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX: 1.491 A, Y: 1.49 A, Z: 1.49 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.4911.491.49
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z894.600894.000894.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-256-255-256
NC/NR/NS512512512
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-22.61534.5720.000
Annotation DetailsReconstruction of an SPP1 capsid after DNA ejection
Supplement
Images
Images
Sample
NameCapsid of SPP1
Number of Components1
Oligomeric StateIcosahedron
Component #1: virus - Bacillus phage SPP1
Scientific nameBacillus phage SPP1
Scientific Name of SpeciesBacillus phage SPP1
NCBI taxonomy10724
EmptyYes
EnvelopedNo
IsolateSPECIES
ClassOTHER
Natural SourceNCBI taxonomy: 1423
Host Species: Bacillus subtilis
Host Category: BACTERIA(EUBACTERIA)
ShellID: 1 , Diameter: 600 A, T Number: 7
Experiment
Sample Preparation
Specimen Support Detailsholey carbon film grids
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
InstrumentFEI VITROBOT MARK I
Imaging
MicroscopeJEOL 2200FS
Date06-APR-2005
DetailsLow-dose imaging procedure
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images94
Sampling Size7
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmAngular reconstitution
SoftwareImagic
CTF CorrectionPhase flipping
Resolution By Author10.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections1200
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-2052.xml (6.4 KB)
Map dataemd_2052.map.gz (119 MB)
ImagesEMD-2052.jpg (226.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2052
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.6 KB