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Icosahedral reconstruction of bacteriophage P4 procapsid

by single particle (icosahedral) reconstruction, at 8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5405
TitleIcosahedral reconstruction of bacteriophage P4 procapsid
MapReconstruction of P4 procapsid
SampleSatellite bacteriophage P4 procapsid
Keywordsbacteriophage, P2, P4, capsid, procapsid, assembly, size determination, scaffolding protein, triangulation numbers, T=7 dextro, Sid, gpN
AuthorsDearborn AD, Laurinmaki P, Chandramouli P, Rodenburg CM, Wang S, Butcher SJ, Dokland T
DateDeposition: 2012-02-20, Header release: 2012-02-22, Map release: 2012-05-29, Last update: 2012-05-29
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

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

Supplemental images
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Article
Citation - Primary
ArticleJ. Struct. Biol., Vol. 178, Issue 3, Page 215-24, Year 2012
TitleStructure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.
AuthorsAltaira D Dearborn, Pasi Laurinmaki, Preethi Chandramouli, Cynthia M Rodenburg, Sifang Wang, Sarah J Butcher, Terje Dokland
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
KeywordsBacteriophage P2 (chemistry), Capsid (chemistry), Cryoelectron Microscopy, Models, Biological, Mutation, Myoviridae (chemistry), Protein Structure, Secondary
LinksPII: S1047-8477(12)00105-0, DOI: 10.1016/j.jsb.2012.04.002, PubMed: 22508104, PMC: PMC3361666
Map
Fileemd_5405.map.gz ( map file in CCP4 format, 39917 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
217 pix
2.73 A/pix
= 592.41 A
217 pix
2.73 A/pix
= 592.41 A
217 pix
2.73 A/pix
= 592.41 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum: -6.67676449 - 11.10193157
Average (Standard dev.): -2E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions217217217
Origin-108-108-108
Limit108108108
Spacing217217217
Unit CellA= B= C: 592.41003 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.73 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.732.732.73
M x/y/z217217217
origin x/y/z0.0000.0000.000
length x/y/z592.410592.410592.410
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-108-108-108
NC/NR/NS217217217
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-6.67711.102-0.000
Annotation DetailsReconstruction of P4 procapsid
Supplement
Images
Images
Sample
NameSatellite bacteriophage P4 procapsid
Number of Components2
Oligomeric State240 copies of gpN and 60 copies of Sid
Theoretical Mass11.268MDa
Component #1: protein - N*, major capsid protein
Scientific namegpN
Common NameN*, major capsid protein
Theoretical Mass9.648 MDa
Oligomeric Detailsicosahedral
Scientific Name of SpeciesEscherichia coli

Common Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainBL21(DE3)
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Vector: pET21
Component #2: protein - external scaffolding protein
Scientific nameSid
Common Nameexternal scaffolding protein
Theoretical Mass1.62 MDa
Oligomeric Detailsicosahedral
Scientific Name of SpeciesEscherichia coli
Common Name of SpeciesE. coli
NCBI taxonomy562
StrainBL21(DE3)
Recombinant expressionYes
Engineered SourceVector: pET21
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Specimen Support Details200 mesh Quantifoil R2/2
Specimen Stateparticle
BufferDetails: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2
pH: 8
Vitrification
MethodBlot for 2 sec before plunging
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
Temperature110 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Date01-JAN-1999
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus900 nm - 3000 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Temperature97 K ( 95 - 99 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerOTHER
Sampling Size4.545
Quant Bit Number8
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmprojection matching, polar Fourier transform
SoftwareEMAN,AUTO3DEM
CTF CorrectionEach micrograph
Resolution By Author8 A
Resolution MethodFSC at 0.25 cutoff
Single Particle
Number of Projections2286
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body fitting of individual subsegments
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3E8K
PDB Chain IDB
Download
Data from EMDB
Header (meta data in XML format)emd-5405.xml (8.6 KB)
Map dataemd_5405.map.gz (22.7 MB)
Imagesemd_5405_1.jpg (111.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5405
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.2 KB