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Structure of a type IV secretion system core complex

by single particle reconstruction, at 18 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.025, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.025, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5035
TitleStructure of a type IV secretion system core complex
Mapvolume
SampletraN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
Keywordsbacterial secretion, type IV secretion, vir, tra
AuthorsFronzes R, Schafer E, Wang L, Saibil H, Orlova E, Waksman G
DateDeposition: 2008-11-10, Header release: 2008-11-18, Map release: 2009-04-15, Last update: 2009-04-15
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.025, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.025, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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EMDB-5032

EMDB-5031

PDB-4b3y
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleScience, Vol. 323, Issue 5911, Page 266-8, Year 2009
TitleStructure of a type IV secretion system core complex.
AuthorsRémi Fronzes, Eva Schäfer, Luchun Wang, Helen R Saibil, Elena V Orlova, Gabriel Waksman
Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
KeywordsBacterial Outer Membrane Proteins (chemistry), Bacterial Proteins (chemistry), Cloning, Molecular, Cryoelectron Microscopy, Gram-Negative Bacteria (chemistry), Imaging, Three-Dimensional, Models, Molecular, Multiprotein Complexes (chemistry), Plasmids, Protein Conformation, Protein Structure, Quaternary, Virulence Factors (chemistry)
LinksDOI: 10.1126/science.1166101, PubMed: 19131631
Map
FileEMD-5035.map ( map file in CCP4 format, 32002 KB )
Projections & SlicesSize of images:
AxesZ (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:0.025, 0.025 (movie #1):
Minimum - Maximum: -0.384705 - 0.385275
Average (Standard dev.): 0.000218033 (0.0162388)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
Unit CellA= B= C: 500 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.52.52.5
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z500.000500.000500.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.3850.3850.000
Annotation Detailsvolume
Supplement
Sample
NametraN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
Number of Components3
Oligomeric State14
Theoretical Mass1.05MDa
Detailsaggregates a high concentration
Mass-estimation Methodgel filtration
Experimental Mass1.1MDa
Component #1: protein - traF
Scientific nametraF
Theoretical Mass0.04 MDa
Oligomeric Details14-mer
Number of Copies14
StrainBL21
Recombinant expressionYes
Natural SourceCell: Escherichia coli
Cell Location: inner membrane
Engineered SourceVector: pASK-IBA3c
NCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - traO
Scientific nametraO
Theoretical Mass0.03 MDa
Oligomeric Details14-mer
Number of Copies14
StrainBL21
Recombinant expressionYes
Natural SourceCell Location: outer membrane
Cell: Escherichia coli
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Vector: pASK-IBA3c
Component #3: protein - traO
Scientific nametraO
Theoretical Mass0.005 MDa
Detailsnon lipidated subunit
Oligomeric Details14-mer
Number of Copies14
StrainBL21
Recombinant expressionYes
Natural SourceCell Location: outer membrane
Cell: Escherichia coli
Engineered SourceVector: pASK-IBA3c
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Staining2% uranyl acetate
Specimen Conc0.5 mg/ml
Specimen Support Detailscarbon coated copper grids
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date01-JAN-2008
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 42000, Calibrated: 42000
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 2000 nm
Specimen Holder
Holderside entry room temperature
ModelOTHER
Temperature293 K ( 293 - 293 K)
Camera
DetectorKodak SO163 film
Image Acquisition
Od Range2
ScannerZEISS SCAI
Number of Digital Images15
Sampling Size7
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmcommon lines
Softwareimagic
Detailsfinal map was calculated from 300 class averages
Resolution By Author18 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages300
Number of Projections1231
Download
Data from EMDB
Header (meta data in XML format)emd-5035.xml (9.3 KB)
Map dataemd_5035.map.gz (1.3 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5035
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, 27.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 27.1 KB