EMDB-1206: Structure of the bacteriophage phi6 nucleocapsid sugge...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1206
Authors	Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 1313.972046, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1313.972046, Made by UCSF CHIMERA
Supplemental images	1206.gif emd_1206_fsc...
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1207 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-5566 EMDB-5567 EMDB-5568 EMDB-5573 EMDB-5572 EMDB-5569 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Structure, Vol. 14, Issue 6, Page 1039-48, Year 2006
Title	Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
Authors	Juha T Huiskonen, Felix de Haas, Doryen Bubeck, Dennis H Bamford, Stephen D Fuller, Sarah J Butcher Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FIN-00014 Helsinki, Finland.
Keywords	Bacteriophage phi 6 (chemistry), Cryoelectron Microscopy, Models, Molecular, Nucleocapsid (chemistry), Nucleocapsid Proteins (chemistry), Protein Conformation, RNA, Double-Stranded (chemistry), RNA, Viral (chemistry), Virus Assembly
Links	PII: S0969-2126(06)00219-X, DOI: 10.1016/j.str.2006.03.018, PubMed: 16765897

Map

File

EMD-1206.map ( map file in CCP4 format, 298474 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	1.8e+03, 1313.972046 (movie #1):
Minimum - Maximum:	-2373 - 4406
Average (Standard dev.):	108.317 (931.766)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	421	421	421
Origin :	-210	-210	-210
Limit :	210	210	210
Spacing :	421	421	421

Unit Cell

A = 589.4 A , B = 589.4 A , C = 589.4 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 1.4 A , Y = 1.4 A , Z = 1.4 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	1.4	1.4	1.4
M x/y/z	421	421	421
origin x/y/z	0.000	0.000	0.000
length x/y/z	589.400	589.400	589.400
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-96	-96	-96
NX/NY/NZ	192	192	192
MAP C/R/S	1	2	3
start NC/NR/NS	-210	-210	-210
NC/NR/NS	421	421	421
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-2373.000	4406.000	108.317

Annotation Details

Reconstruction of phi6 nucleocapsid to 7.5-A resolution

Supplement

Mask Set

Mask: #0

File

EMD-1206.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

210 , 210 , 210

Origin

-74 , -61 , 64

Limit

135 , 148 , 273

Spacing

210 , 210 , 210

Cell

A = 294.0 A , B = 294.0 A , C = 294.0 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.0042690854 , std. = 0.06519862

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:1::::

Pixel Spacing

X = 1.4 A , Y = 1.4 A , Z = 1.4 A

Annotation Details

tc_B

Mask: #1

File

EMD-1206_1.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.031976536 , std. = 0.1759376

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:2::::

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

Alpha subunit

Mask: #2

File

EMD-1206_2.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.03180958 , std. = 0.17549282

Details

bmask -datatype s -verbose 7 -threshold 0.5 phi6nc_421_B_mask_I.map phi6nc_421_B _mask_I.map

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

Beta subunit

Mask: #3

File

EMD-1206_3.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.024569845 , std. = 0.1548101

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:4::::

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

Q subunit

Mask: #4

File

EMD-1206_4.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.024228562 , std. = 0.15375805

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:5::::

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

R subunit

Mask: #5

File

EMD-1206_5.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.023665056 , std. = 0.15200336

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:6::::

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

S subunit

Mask: #6

File

EMD-1206_6.msk ( map file in CCP4 format, KB )

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

Data Type

Image stored as Integer*2

Dimensions

421 , 421 , 421

Origin

-210 , -210 , -210

Limit

210 , 210 , 210

Spacing

421 , 421 , 421

Cell

A = 589.39996 A , B = 589.39996 A , C = 589.39996 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Axis Order

X - Y - Z

Statistics

min. = 0.0 , max. = 1.0 , avg. = 0.0072074924 , std. = 0.08459045

Space Group Number

Details

::::EMDATABANK.org::::EMD-1206::::MASK:7::::

Pixel Spacing

X = 1.3999999 A , Y = 1.3999999 A , Z = 1.3999999 A

Annotation Details

T subunit

Images

1206.gif

Others

Details

[MASKnames]
emd_1206_msk_1.map > phi6nc_210_tc_B_mask.map
emd_1206_msk_2.map > phi6nc_421_A_mask.map
emd_1206_msk_3.map > phi6nc_421_B_mask.map
emd_1206_msk_4.map > phi6nc_421_Q_mask.map
emd_1206_msk_5.map > phi6nc_421_R_mask.map
emd_1206_msk_6.map > phi6nc_421_S_mask.map
emd_1206_msk_7.map > phi6nc_421_T_mask.ma

Image

File: emd_1206_fsc.jpg

Sample
Name	Bacteriophage phi6 nucleocapsid
Number of Components	1
Theoretical Mass	22 MDa
Component #1: virus - Bacteriophage phi6
Scientific name	Pseudomonas phage phi6
Common Name	Bacteriophage phi6
Scientific Name of Species	Pseudomonas phage phi6 (NCBI Taxonomy: 10879)
Common Name of Species	Bacteriophage phi6
Empty	No
Enveloped	Yes
Isolate	SPECIES
Class	VIRION
Natural Source	Host Species: Pseudomonas syringae pv phaesolicola HB10Y Host Category: BACTERIA(EUBACTERIA)
Shell	Diameter: 485 A Name Element: PC shell T Number: 1
Shell	Diameter: 555 A T Number: 13 Name Element: NC shell

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Imaging
Microscope	FEI TECNAI F20
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Astigmatism	objective lens astigmatism was corrected at
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	400 nm - 2500 nm
Specimen Holder
Holder	Side entry liquid nitrogen-cooled cryo specimen holder ( OTHER )
Tilt Angle	0 degrees - 0 degrees
Temperature	93 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	52
Sampling Size	7 microns
Quant Bit Number	12
Scanner	ZEISS SCAI

Processing
Method	single particle (icosahedral) reconstruction
3 D reconstruction
Algorithm	POR orientation search, 3D reconstruction in Cartesian coordinates using P3DR
Software	P3DR
CTF Correction	each particle, full CTF correction
Resolution By Author	7.5
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	10463
Applied Symmetry	I (icosahedral)