EMDB-1011: Minor proteins, mobile arms and membrane-capsid intera...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1011
Authors	San Martin C, Huiskonen JT, Bamford JK, Butcher SJ, Fuller SD, Bamford DH, Burnett RM
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 6317.146470904, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 6317.146470904, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1gw7, Surface level: 6317.146470904, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-1gw7, Surface level: 9000, Made by UCSF CHIMERA #5: Simplified surface model with fitted atomic model: PDB-1gw7, Made by Jmol
Supplemental images	1011.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1gw7 CiteFit EMDB-1012 Cite PDB-1gw8 Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1123 EMDB-1012 EMDB-1339 EMDB-1557 EMDB-2049 EMDB-1013 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Struct. Biol., Vol. 9, Issue 10, Page 756-63, Year 2002
Title	Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Authors	Carmen San Martín, Juha T Huiskonen, Jaana K H Bamford, Sarah J Butcher, Stephen D Fuller, Dennis H Bamford, Roger M Burnett The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.
Keywords	Bacteriophage PRD1 (genetics), Capsid (metabolism), Cloning, Molecular, Crystallography, X-Ray, Intracellular Membranes (metabolism), Models, Molecular
Links	PubMed: 12219080, DOI: 10.1038/nsb837

Map

File

EMD-1011.map ( map file in CCP4 format, 67109.888 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:	7.77e+03, 6317.1464709 (movie #1):
Minimum - Maximum:	-16843.7 - 27000
Average (Standard dev.):	188.248 (3602.72)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	256	256	256
Origin :	-127	-127	-127
Limit :	128	128	128
Spacing :	256	256	256

Unit Cell

A = 880.64 A , B = 880.64 A , C = 880.64 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 3.44 A , Y = 3.44 A , Z = 3.44 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	3.44	3.44	3.44
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	880.640	880.640	880.640
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	-127	-127	-127
NC/NR/NS	256	256	256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-16843.711	27000.000	188.248

Annotation Details

This map is one of four described in San Martin, C., Huiskonen, J. T., Bamford, J. K., Butcher, S. J., Fuller, S. D., Bamford, D. H., and Burnett, R. M. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol 9, 756-763. The other three maps are also available.

Supplement
Slice Set
Slice: #0
File	EMD-1011.slc ( map file in CCP4 format, 263.168 KB )
Data Type	float (32-bit)
Dimensions	256 , 256 , 1
Origin	-127 , -127 , 0
Limit	128 , 128 , 0
Spacing	256 , 256 , 0
Cell	A = 256.000 A , B = 256.000 A , C = 1.000 A , alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees
Axis Order	X - Y - Z
Statistics	min. = -15940.52344 , max. = 24043.01367 , avg. = 656.55023 , std. = 0.00000
Space Group Number	1
Details	Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:30:08
Pixel Spacing	X = 3.44 A , Y = 3.44 A , Z = 3.44 A
Slice: #1
File	EMD-1011_1.slc ( map file in CCP4 format, 263.168 KB )
Data Type	float (32-bit)
Dimensions	256 , 256 , 1
Origin	-127 , -127 , 0
Limit	128 , 128 , 0
Spacing	256 , 256 , 0
Cell	A = 256.000 A , B = 256.000 A , C = 1.000 A , alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees
Axis Order	X - Y - Z
Statistics	min. = -15709.90234 , max. = 24138.25000 , avg. = 652.49756 , std. = 0.00000
Space Group Number	1
Details	Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:31:02
Pixel Spacing	X = 3.44 A , Y = 3.44 A , Z = 3.44 A
Slice: #2
File	EMD-1011_2.slc ( map file in CCP4 format, 263.168 KB )
Data Type	float (32-bit)
Dimensions	256 , 256 , 1
Origin	-127 , -127 , 0
Limit	128 , 128 , 0
Spacing	256 , 256 , 0
Cell	A = 256.000 A , B = 256.000 A , C = 1.000 A , alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees
Axis Order	X - Y - Z
Statistics	min. = -15620.57227 , max. = 24412.70703 , avg. = 653.29291 , std. = 0.00000
Space Group Number	1
Details	Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:31:39
Pixel Spacing	X = 3.44 A , Y = 3.44 A , Z = 3.44 A
Images
Images	1011.gif

Sample
Name	Bacteriophage PRD1
Oligomeric State	A pseudo T=25 assembly
Number of Components	1
Theoretical Mass	70 MDa
Details	The sample is a virion containing at least 19 structural proteins and a double stranded DNA genome
Component #1: virus - bacteriophage PRD1
Scientific name	Enterobacteria phage PRD1
Common Name	bacteriophage PRD1
Details	a T=25 virion
Scientific Name of Species	Enterobacteria phage PRD1 (NCBI Taxonomy: 10658)
Common Name of Species	bacteriophage PRD1
Empty	No
Enveloped	No
Isolate	STRAIN
Class	VIRION
Natural Source	Host Species: Salmonella enterica (NCBI Taxonomy: 28901) Host Category: BACTERIA(EUBACTERIA)
Shell	Diameter: 70 A Name Element: P3 T Number: 25

Experiment
Sample Preparation
Specimen Conc	1 mg/ml
Specimen State	particle
Buffer	Details: 20 mM Tris HCl pH: 7.2
Vitrification
Cryogen Name	ETHANE
Humidity	60
Temperature	23 Kelvin
Instrument	HOMEMADE PLUNGER
Method	Blot for 1 s before plunging into ethane slush
Details	Vitrification instrument: EMBL plunger. vitrification carried out at 23 degrees at ambient humidity
Imaging
Microscope	FEI/PHILIPS CM200FEG/ST
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	6 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 36000 X,
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1300 nm - 4100 nm
Specimen Holder
Holder	eucentric ( GATAN LIQUID NITROGEN )
Temperature	105 Kelvin
Camera
Detector	SO163
Distance	44
Image Acquisition
Number of Digital Images	50
Sampling Size	7.0 microns
Od Range	1
Quant Bit Number	8
Scanner	ZEISS SCAI
Details	images were scanned at 7 micron steps size and then averaged to give a final size of 14 microns

Processing
Method	single particle (icosahedral) reconstruction
3 D reconstruction
Algorithm	Fourier-Bessel
Software	EMBL-ICOS, MRC
CTF Correction	normalized sum of ctf multiplied images
Resolution By Author	16
Resolution Method	16
Euler Angles Details	range giving min eigenvalues for inversion of less than .01
Details	final maps were calculated by making a normalized sum of seperate ctf multiplied maps Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs. Microbiology and Molecular Biology Reviews 63, 862-922. Butcher, S. J., Bamford, D. H., and Fuller, S. D. (1995). DNA packaging orders the membrane of bacteriophage PRD1. Embo J 14, 6078-6086. Ferlenghi, I., Gowen, B., de Haas, F., Mancini, E. J., Garoff, H., Sjoberg, M., and Fuller, S. D. (1998). The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike. J Mol Biol 283, 71-81. Fuller, S. D., Berriman, J. A., Butcher, S. J., and Gowen, B. E. (1995). Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81, 715-725. Fuller, S. D., Butcher, S. J., Cheng, R. H., and Baker, T. S. (1996). Three-dimensional reconstruction of icosahedral particles--the uncommon line. J Struct Biol 116, 48-55. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T., and Fuller, S. D. (2000). Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Molecular Cell 5, 255-266. Mancini, E. J., de Haas, F., and Fuller, S. D. (1997). High-resolution icosahedral reconstruction: fulfilling the promise of cryo-electron microscopy. Structure 5, 741-750. San Martin, C., Burnett, R. M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S. D., Butcher, S. J., and Bamford, D. H. (2001). Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure (Camb) 9, 917-930. San Martin, C., Huiskonen, J. T., Bamford, J. K., Butcher, S. J., Fuller, S. D., Bamford, D. H., and Burnett, R. M. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol 9, 756-763. Sheehan, B., Fuller, S. D., Pique, M. E., and Yeager, M. (1996). AVS software for visualization in molecular microscopy. J Struct Biol 116, 99-106.
Single Particle
Number of Projections	1468
Details	The particles were purified by rate-zonal centrifugation and ion-exchange chromatography Walin,Tuma,Thomas and Bamford Virology (1994) 201:1-7
Applied Symmetry	I (icosahedral)
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Target Criteria	minimizing R factor (final 47.7%)
Software	emfit (M. Rossmann Cheng, R., Kuhn, R., Olson, N., Rossmann, M., and Baker, T. (1995). Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80, 621-630.)
Details	Protocol: real space refinement. The scale of the map and the effective resolution were determined from a comparison between the P3 portion of the WT reconstruction and the atomic model
Fitted Coordinate
PDB entry ID	PDB-1gw7

Download

Data from EMDB

Header (meta data in XML format)

emd-1011.xml (18.8 KB)

Map data

emd_1011.map.gz (59.1 MB)

Images

1011.gif (24.9 KB)

Slices

emd_1011_1_slc.map (257 KB)

emd_1011_2_slc.map (257 KB)

emd_1011_3_slc.map (257 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1011

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.6 MB Session file for UCSF-Chimera, 20.2 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.5 MB Session file for UCSF-Chimera, 20.4 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 1.9 MB .webm (WebM/VP8 format), 2.9 MB Session file for UCSF-Chimera, 3.5 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 1.9 MB .webm (WebM/VP8 format), 3 MB Session file for UCSF-Chimera, 6.7 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.9 MB .webm (WebM/VP8 format), 5.9 MB