EMDB-5405: Icosahedral reconstruction of bacteriophage P4 procapsid

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5405
Title	Icosahedral reconstruction of bacteriophage P4 procapsid
Map	Reconstruction of P4 procapsid
Sample	Satellite bacteriophage P4 procapsid
Keywords	bacteriophage, P2, P4, capsid, procapsid, assembly, size determination, scaffolding protein, triangulation numbers, T=7 dextro, Sid, gpN
Authors	Dearborn AD, Laurinmaki P, Chandramouli P, Rodenburg CM, Wang S, Butcher SJ, Dokland T
Date	Deposition: 2012-02-20, Header release: 2012-02-22, Map release: 2012-05-29, Last update: 2012-05-29
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 2, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5406 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-2184 EMDB-1120 EMDB-1116 EMDB-1154 EMDB-1611 List of similar structure data about Omokage system

Article
Citation - Primary
Article	J. Struct. Biol., Vol. 178, Issue 3, Page 215-24, Year 2012
Title	Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.
Authors	Altaira 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.
Keywords	Bacteriophage P2 (chemistry), Capsid (chemistry), Cryoelectron Microscopy, Models, Biological, Mutation, Myoviridae (chemistry), Protein Structure, Secondary
Links	PII: S1047-8477(12)00105-0, DOI: 10.1016/j.jsb.2012.04.002, PubMed: 22508104, PMC: PMC3361666

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 = 592.41003 A , B = 592.41003 A , C = 592.41003 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.73 A , Y = 2.73 A , Z = 2.73 A

CCP4 map header info

Annotation Details

Reconstruction of P4 procapsid

Sample
Name	Satellite bacteriophage P4 procapsid
Number of Components	2
Oligomeric State	240 copies of gpN and 60 copies of Sid
Theoretical Mass	11.268 MDa
Component #1: protein - N*, major capsid protein
Scientific name	gpN
Common Name	N*, major capsid protein
Theoretical Mass	9.648 MDa
Oligomeric Details	icosahedral
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Common Name of Species	Escherichia coli
Strain	BL21(DE3)
Recombinant expression	Yes
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562) Vector: pET21
Component #2: protein - external scaffolding protein
Scientific name	Sid
Common Name	external scaffolding protein
Theoretical Mass	1.62 MDa
Oligomeric Details	icosahedral
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Common Name of Species	E. coli
Strain	BL21(DE3)
Recombinant expression	Yes
Engineered Source	Vector: pET21 Exp System: Escherichia coli (NCBI Taxonomy: 562)

Experiment
Sample Preparation
Specimen Conc	1.0 mg/ml
Specimen Support Details	200 mesh Quantifoil R2/2
Specimen State	particle
Buffer	Details: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2 pH: 8.0
Vitrification
Method	Blot for 2 sec before plunging
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Temperature	110 Kelvin
Imaging
Microscope	FEI TECNAI F20
Date	01-JAN-1999
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50000 X
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	900 nm - 3000 nm
Specimen Holder
Holder	( GATAN LIQUID NITROGEN )
Temperature	97 Kelvin ( 95 Kelvin - 99 Kelvin )
Camera
Detector	Kodak SO-163 film
Image Acquisition
Scanner	OTHER
Sampling Size	4.545 microns
Quant Bit Number	8

Processing
Method	single particle (icosahedral) reconstruction
3 D reconstruction
Algorithm	projection matching, polar Fourier transform
Software	EMAN,AUTO3DEM
CTF Correction	Each micrograph
Resolution By Author	8.0
Resolution Method	FSC at 0.25 cutoff
Single Particle
Number of Projections	2286
Applied Symmetry	I (icosahedral)
Atomic Model Fitting
Model #0
Details	Protocol: Rigid body fitting of individual subsegments
Software	Chimera
Refinement Protocol	rigid body
Refinement Space	REAL

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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