EMDB-2136: Negative stain EM composite structure (part 1) of the ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 2136
Title	Negative stain EM composite structure (part 1) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10
Map	Core complex part of the VirB4-core complex composite reconstruction
Sample	TraB/TraN/TraO/TraF complex encoded by pKM101
Authors	Williams R, Wallden K, Yan J, Lian PW, Wang L, Thalassinos K, Orlova EV, Waksman G
Date	Deposition: 2012-06-12, Header release: 2012-07-25, Map release: 2012-08-01, Last update: 2012-08-29
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.25, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.25, Made by UCSF CHIMERA
Supplemental images	EMD2136.tif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-2137 Cite PDB-4ag5 Cite PDB-4ag6 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-5031 EMDB-5032 EMDB-5033 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 28, Page 11348-53, Year 2012
Title	Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
Authors	Karin Walldén, Robert Williams, Jun Yan, Pei W Lian, Luchun Wang, Konstantinos Thalassinos, Elena V Orlova, Gabriel Waksman Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, London WC1E 7HX, United Kingdom.
Keywords	Adenosine Triphosphatases (chemistry, 3.6.1.-), Bacterial Proteins (chemistry), Binding Sites, Crystallization, Crystallography, X-Ray (methods), DNA, Bacterial (genetics), Escherichia coli (metabolism), Macromolecular Substances (metabolism), Magnesium (chemistry, 7439-95-4), Mass Spectrometry (methods), Microscopy, Electron (methods), Models, Biological, Nucleotides (chemistry), Plasmids, Protein Binding, Protein Conformation, Virulence Factors (genetics)
Links	DOI: 10.1073/pnas.1201428109, PubMed: 22745169, PMC: PMC3396474

Map

File

EMD-2136.map ( map file in CCP4 format, 62502 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:	0.35 (by emdb), 0.25 (movie #1):
Minimum - Maximum:	-1.48925638 - 1.98086631
Average (Standard dev.):	0.0111697 (0.09054922)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	250	250	250
Origin	-125	-125	-125
Limit	124	124	124
Spacing	250	250	250

Unit Cell

A= B= C: 417.5 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 1.67 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	1.67	1.67	1.67
M x/y/z	250	250	250
origin x/y/z	0.000	0.000	0.000
length x/y/z	417.500	417.500	417.500
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-32	-32	-32
NX/NY/NZ	64	64	64
MAP C/R/S	1	2	3
start NC/NR/NS	-125	-125	-125
NC/NR/NS	250	250	250
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-1.489	1.981	0.011

Annotation Details

Core complex part of the VirB4-core complex composite reconstruction

Supplement
Images
Images	EMD2136.tif

Sample
Name	TraB/TraN/TraO/TraF complex encoded by pKM101
Number of Components	4
Oligomeric State	14-mer of core complex (TraN/TraO/TraF) and monomer of TraB
Theoretical Mass	1.15MDa
Experimental Mass	1.15MDa
Component #1: protein - VirB4
Scientific name	TraB
Common Name	VirB4
Details	The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies	1
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	pKM101 plasmid
Recombinant expression	Yes
Natural Source	Cell Location: cell envelope
Engineered Source	Vector: pASK IBA3C NCBI taxonomy: 562 Expression system: Escherichia coli
Component #2: protein - VirB7
Scientific name	TraN
Common Name	VirB7
Details	The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies	14
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	pKM101 plasmid
Recombinant expression	Yes
Natural Source	Cell Location: cell envelope
Engineered Source	NCBI taxonomy: 562 Expression system: Escherichia coli Vector: pASK IBA3C
Component #3: protein - VirB9
Scientific name	TraO
Common Name	VirB9
Details	The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies	14
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	pKM101 plasmid
Recombinant expression	Yes
Natural Source	Cell Location: cell envelope
Engineered Source	Vector: pASK IBA3C NCBI taxonomy: 562 Expression system: Escherichia coli
Component #4: protein - VirB10
Scientific name	TraF
Common Name	VirB10
Details	The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies	14
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	pKM101 plasmid
Recombinant expression	Yes
Natural Source	Cell Location: cell envelope
Engineered Source	Vector: pASK IBA3C NCBI taxonomy: 562 Expression system: Escherichia coli

Experiment
Sample Preparation
Staining	NanoW
Specimen Support Details	Glow-discharged continuous carbon
Specimen State	particle
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI 12
Date	22-DEC-2009
Electron Gun
Electron Source	OTHER
Accelerating Voltage	120 kV
Illumination Mode	SPOT SCAN
Lens
Magnification	Nominal: 42000
Imaging Mode	BRIGHT FIELD
Defocus	700 nm - 2000 nm
Specimen Holder
Model	SIDE ENTRY, EUCENTRIC
Tilt Angle	0 degrees - 0 degrees
Camera
Detector	Zeiss SCAI microdensitometer
Image Acquisition
Scanner	ZEISS SCAI
Number of Digital Images	12
Sampling Size	7
Quant Bit Number	8

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Common lines
Software	IMAGIC
Details	This map is part of a composite structure of two maps.
Resolution By Author	20 A
Resolution Method	FSC at cutoff 0.5
Single Particle
Number of Class Averages	330
Number of Projections	10000

Download

Data from EMDB

Header (meta data in XML format)

emd-2136.xml (9.9 KB)

Map data

emd_2136.map.gz (4.3 MB)

Images

EMD2136.tif (74.2 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2136

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.7 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 26.7 KB