EMDB-1048: Three-dimensional structure of bacteriophage T4 baseplate.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1048
Authors	Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, vanRaaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG
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 cylindrical radius, Surface level: 2, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w, Surface level: 2, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1pdf, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-1pdi, Made by Jmol #6: Simplified surface model with fitted atomic model: PDB-1pdj, Made by Jmol #7: Simplified surface model with fitted atomic model: PDB-1pdl, Made by Jmol #8: Simplified surface model with fitted atomic model: PDB-1pdm, Made by Jmol #9: Simplified surface model with fitted atomic model: PDB-1pdp, Made by Jmol #10: Simplified surface model with fitted atomic model: PDB-2fl8, Made by Jmol #11: Simplified surface model with fitted atomic model: PDB-3h3w, Made by Jmol
Supplemental images	1048.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1pdf CiteFit PDB-1pdi CiteFit PDB-1pdj CiteFit PDB-1pdl CiteFit PDB-1pdm CiteFit PDB-1pdp CiteFit PDB-2fl8 Fit PDB-3h3w Fit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-5330 EMDB-1152 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Struct. Biol., Vol. 10, Issue 9, Page 688-93, Year 2003
Title	Three-dimensional structure of bacteriophage T4 baseplate.
Authors	Victor A Kostyuchenko, Petr G Leiman, Paul R Chipman, Shuji Kanamaru, Mark J van Raaij, Fumio Arisaka, Vadim V Mesyanzhinov, Michael G Rossmann Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia.
Keywords	Bacteriophage T4 (chemistry), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Microscopy, Electron, Models, Molecular, Protein Structure, Tertiary
Links	PubMed: 12923574, DOI: 10.1038/nsb970

Map

File

EMD-1048.map ( map file in CCP4 format, 30119 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:	1.45 (by author), 2 (movie #1):
Minimum - Maximum:	-7.64827013 - 10.34481144
Average (Standard dev.):	0E-8 (1.00000000)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	196	196	196
Origin :	-98	-98	-97
Limit :	97	97	98
Spacing :	196	196	196

Unit Cell

A = 583.8291 A , B = 583.8291 A , C = 583.8291 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.97872 A , Y = 2.97872 A , Z = 2.97872 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.9787193877551	2.9787193877551	2.9787193877551
M x/y/z	196	196	196
origin x/y/z	0.000	0.000	0.000
length x/y/z	583.829	583.829	583.829
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	0	0	52
NX/NY/NZ	128	128	55
MAP C/R/S	1	2	3
start NC/NR/NS	-98	-98	-97
NC/NR/NS	196	196	196
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-7.648	10.345	0.000

Annotation Details

map contains the baseplate and the proximal part of the tail tube

Supplement
Images
Images	1048.gif

Sample
Name	Bacteriophage T4 baseplate-tail tube assembly
Number of Components	1
Oligomeric State	the complex has sixfold symmetry
Component #1: protein - baseplate-tail tube complex
Scientific name	baseplate-tail tube complex
Scientific Name of Species	Enterobacteria phage T4 (NCBI Taxonomy: 10665)
Common Name of Species	bacteriophage T4
Strain	T4 18-,23-
Recombinant expression	Yes
Natural Source	Organelle: baseplate and tail tube
Engineered Source	Exp System: Escherichia coli BE

Experiment
Sample Preparation
Specimen Conc	5 mg/ml
Specimen Support Details	holey carbon
Specimen State	particle
Buffer	Details: water pH: 7
Vitrification
Cryogen Name	ETHANE
Method	Blot for 2 seconds before plunging
Imaging
Microscope	FEI/PHILIPS CM300FEG/T
Date	2001-01-30
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	25 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 45000 X, Calibrated: 47000 X
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1200 nm - 5000 nm
Specimen Holder
Holder	626 Single Tilt Cryotransfer System ( GATAN LIQUID NITROGEN )
Tilt Angle	0 degrees - 0 degrees
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	15
Sampling Size	14 microns
Quant Bit Number	8
Scanner	ZEISS SCAI
Details	images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	model based projection matching
Software	SPIDER
CTF Correction	each particle
Details	modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
Resolution By Author	12.0
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	945
Atomic Model Fitting
Model #0
Details	Protocol: laplacian filtered real space
Refinement Protocol	rigid body
Target Criteria	correlation coefficient
Refinement Space	REAL
Software	Situs 2.0, Colores
Model #1
Software	Situs 2.0, Colores
Target Criteria	correlation coefficient
Details	Protocol: laplacian filtered real space
Refinement Protocol	rigid body
Refinement Space	REAL
Model #2
Target Criteria	correlation coefficient
Refinement Space	REAL
Software	Situs 2.0, Colores
Refinement Protocol	rigid body
Details	Protocol: laplacian filtered real space
Model #3
Refinement Protocol	rigid body
Refinement Space	REAL
Software	Situs 2.0, Colores
Details	Protocol: laplacian filtered real space
Target Criteria	correlation coefficient
Model #4
Details	Protocol: laplacian filtered real space
Target Criteria	correlation coefficient
Refinement Protocol	rigid body
Refinement Space	REAL
Software	Situs 2.0, Colores
Model #5
Software	Situs 2.0, Colores
Refinement Protocol	rigid body
Details	Protocol: laplacian filtered real space
Target Criteria	correlation coefficient
Refinement Space	REAL
Model #6
Refinement Space	REAL
Target Criteria	correlation coefficient
Software	Situs 2.0, Colores
Details	Protocol: laplacian filtered real space
Refinement Protocol	rigid body
Model #7
Target Criteria	correlation coefficient
Refinement Space	REAL
Refinement Protocol	rigid body
Software	Situs 2.0, Colores
Details	Protocol: laplacian filtered real space
Fitted Coordinate
PDB entry ID	PDB-1pdf PDB-1pdi PDB-1pdj PDB-1pdl PDB-1pdm PDB-1pdp PDB-2fl8 PDB-3h3w

Download

Data from EMDB

Header (meta data in XML format)

emd-1048.xml (10.3 KB)

Map data

emd_1048.map.gz (3.5 MB)

Images

1048.gif (53.1 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1048

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.8 MB Session file for UCSF-Chimera, 26.8 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.1 MB .webm (WebM/VP8 format), 4.4 MB Session file for UCSF-Chimera, 26.8 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.1 MB Session file for UCSF-Chimera, 6.9 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.3 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.8 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.2 MB

movie #7

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.8 MB

movie #8

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.7 MB

movie #9

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.5 MB

movie #10

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.6 MB

movie #11

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5 MB