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A cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.

by single particle reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.33535264, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 2.33535264, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5009
TitleA cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.
Map3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
SampleFimD-tip complex
Keywordscryo-electron microscopy, bacterial pilus, bacterial outer membrane secretion channel, pilus biogenesis
AuthorsTang C, Thanassi D, Li H
DateDeposition: 2008-03-14, Header release: 2008-03-21, Map release: 2009-04-22, Last update: 2009-04-22
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.33535264, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 2.33535264, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-2vqi
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-2241

EMDB-2156
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell, Vol. 133, Issue 4, Page 640-52, Year 2008
TitleFiber formation across the bacterial outer membrane by the chaperone/usher pathway.
AuthorsHan Remaut, Chunyan Tang, Nadine S Henderson, Jerome S Pinkner, Tao Wang, Scott J Hultgren, David G Thanassi, Gabriel Waksman, Huilin Li
Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom.
KeywordsAmino Acid Sequence, Biosynthetic Pathways, Crystallography, X-Ray, Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), Fimbriae Proteins (chemistry, 147680-16-8), Fimbriae, Bacterial (ultrastructure), Models, Molecular, Molecular Chaperones (metabolism), Molecular Sequence Data, Multiprotein Complexes (chemistry), Porins (chemistry), atpG protein, E coli, fimC protein, E coli, fimD protein, E coli
LinksPII: S0092-8674(08)00462-5, DOI: 10.1016/j.cell.2008.03.033, PubMed: 18485872, PMC: PMC3036173
Map
FileEMD-5009.map ( map file in CCP4 format, 3540 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:1.74, 2.3353526 (movie #1):
Minimum - Maximum: -4.68613 - 8.0905
Average (Standard dev.): 6.58932e-09 (0.871601)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin-48-48-48
Limit474747
Spacing969696
Unit CellA= B= C: 241.3 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.54 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.542.542.54
M x/y/z959595
origin x/y/z0.0000.0000.000
length x/y/z241.300241.300241.300
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.6868.0910.000
Annotation Details3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Supplement
Sample
NameFimD-tip complex
Number of Components5
Oligomeric StateFimD usher dimer in complex with one copy each of FimH, FimF, FimG pilins and FimC chaperone
Theoretical Mass0.26MDa
DetailsThe sample was monodisperse
Experimental Mass0.26MDa
Component #1: cellular-component - Pilus assembly usher
Scientific nameFimD-tip complex
Common NamePilus assembly usher
Theoretical Mass0.096 MDa
Experimental Mass0.096 MDa
DetailsThis component forms a dimer in the complex
Oligomeric DetailsDimer
Number of Copies1
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: Outer membrane
Engineered SourceVector: Tuner/pAN2 and pNH237
Expression system: Escherichia coli B strain Tuner (Novagen)
LinksGene Ontology: GO:0015473, Inter Pro: IPR:000015
Experiment
Sample Preparation
Specimen Conc0.04 mg/ml
Specimen Support Detailsglow-discharged lacey carbon grid
Specimen Stateparticle
BufferDetails: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
pH: 8
Vitrification
Method6 seconds blot
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot. 12 degree Celsius chamber temperature
Humidity85
InstrumentFEI VITROBOT
Temperature108 Kelvin
Imaging
MicroscopeJEOL 2010F
Date01-Feb-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Electron Beam Tilt Params-2 mrad
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Astigmatismcorrection at 250,000 mag
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus3000 nm - 5000 nm
Specimen Holder
HolderGatan 626 cryo holder
ModelGATAN LIQUID NITROGEN
Temperature103 K ( 100 - 105 K)
Camera
DetectorKodak SO163
Image Acquisition
Od Range1.3
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images100
Sampling Size12.7
Quant Bit Number14
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCross-common lines
SoftwareEMAN, SPIDER
CTF CorrectionEach films
Resolution By Author23 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages100
Number of Projections11000
Detailsparticles were manually selected
Atomic Model Fitting
Model #0
Target Criteriacorrelation
DetailsProtocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID1QUN

PDB-1qun
PDB Chain ID1QUN_A
Download
Data from EMDB
Header (meta data in XML format)emd-5009.xml (8.6 KB)
Map dataemd_5009.map.gz (3 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5009
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 19.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.2 MB
Session file for UCSF-Chimera, 19.6 KB