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Negative stain EM composite structure (part 1) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.25, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.25, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2136
TitleNegative stain EM composite structure (part 1) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10
MapCore complex part of the VirB4-core complex composite reconstruction
SampleTraB/TraN/TraO/TraF complex encoded by pKM101
AuthorsWilliams R, Wallden K, Yan J, Lian PW, Wang L, Thalassinos K, Orlova EV, Waksman G
DateDeposition: 2012-06-12, Header release: 2012-07-25, Map release: 2012-08-01, Last update: 2012-08-29
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.25, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.25, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 28, Page 11348-53, Year 2012
TitleStructure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
AuthorsKarin 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.
KeywordsAdenosine 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), Mass Spectrometry (methods), Microscopy, Electron (methods), Models, Biological, Nucleotides (chemistry), Plasmids, Protein Binding, Protein Conformation, Virulence Factors (genetics)
LinksDOI: 10.1073/pnas.1201428109, PubMed: 22745169, PMC: PMC3396474
Map
Fileemd_2136.map.gz ( map file in CCP4 format, 61037 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.67 A/pix
= 417.5 A
250 pix
1.67 A/pix
= 417.5 A
250 pix
1.67 A/pix
= 417.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.35 (by emdb), 0.25 (movie #1):
Minimum - Maximum: -1.48925638 - 1.98086631
Average (Standard dev.): 0.0111697 (0.09054922)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin-125-125-125
Limit124124124
Spacing250250250
Unit CellA= B= C: 417.5 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.67 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.671.671.67
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z417.500417.500417.500
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.4891.9810.011
Annotation DetailsCore complex part of the VirB4-core complex composite reconstruction
Supplement
Images
Images
Sample
NameTraB/TraN/TraO/TraF complex encoded by pKM101
Number of Components4
Oligomeric State14-mer of core complex (TraN/TraO/TraF) and monomer of TraB
Theoretical Mass1.15MDa
Experimental Mass1.15MDa
Component #1: protein - VirB4
Scientific nameTraB
Common NameVirB4
DetailsThe 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies1
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
StrainpKM101 plasmid
Recombinant expressionYes
Natural SourceCell Location: cell envelope
Engineered SourceVector: pASK IBA3C
NCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - VirB7
Scientific nameTraN
Common NameVirB7
DetailsThe 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies14
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainpKM101 plasmid
Recombinant expressionYes
Natural SourceCell Location: cell envelope
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Vector: pASK IBA3C
Component #3: protein - VirB9
Scientific nameTraO
Common NameVirB9
DetailsThe 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies14
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainpKM101 plasmid
Recombinant expressionYes
Natural SourceCell Location: cell envelope
Engineered SourceVector: pASK IBA3C
NCBI taxonomy: 562
Expression system: Escherichia coli
Component #4: protein - VirB10
Scientific nameTraF
Common NameVirB10
DetailsThe 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies14
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainpKM101 plasmid
Recombinant expressionYes
Natural SourceCell Location: cell envelope
Engineered SourceVector: pASK IBA3C
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
StainingNanoW
Specimen Support DetailsGlow-discharged continuous carbon
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date22-DEC-2009
Electron Gun
Electron SourceOTHER
Accelerating Voltage120 kV
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 42000
Imaging ModeBRIGHT FIELD
Defocus700 nm - 2000 nm
Specimen Holder
ModelSIDE ENTRY, EUCENTRIC
Tilt Angle0 degrees - 0 degrees
Camera
DetectorGENERIC FILM
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images12
Sampling Size7
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCommon lines
SoftwareIMAGIC
DetailsThis map is part of a composite structure of two maps.
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages330
Number of Projections10000
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-2136.xml (9.9 KB)
Map dataemd_2136.map.gz (4.3 MB)
ImagesEMD2136.tif (74.2 KB)
FTP directoryftp://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