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- EMDB-5009: A cryo-EM map of the FimD-tip complex, a bacterial surface pilus ... -

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Basic information

Entry
Database: EMDB / ID: 5009
TitleA cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.
Keywordscryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis
SampleFimD-tip complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Methodsingle particle reconstruction, at 23 A resolution
AuthorsTang C / Thanassi D / Li H
CitationCell, 2008, 133, 640-652

Cell, 2008, 133, 640-652 StrPapers
Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
Han Remaut / Chunyan Tang / Nadine S Henderson / Jerome S Pinkner / Tao Wang / Scott J Hultgren / David G Thanassi / Gabriel Waksman / Huilin Li

DateDeposition: Mar 14, 2008 / Header (metadata) release: Mar 21, 2008 / Map release: Apr 22, 2009 / Last update: Mar 14, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.33535264
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 2.33535264
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_5009.map.gz (map file in CCP4 format, 3457 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
2.54 A/pix
= 241.3 A
96 pix
2.54 A/pix
= 241.3 A
96 pix
2.54 A/pix
= 241.3 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.54 A
Density
Contour Level:1.74, 2.3353526 (movie #1):
Minimum - Maximum-4.68613 - 8.0905
Average (Standard dev.)6.58932e-09 (0.871601)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin-48-48-48
Limit474747
Spacing969696
CellA=B=C: 241.3 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-4.6868.0910.000

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Supplemental data

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Sample components

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Entire FimD-tip complex

EntireName: FimD-tip complex / Details: The sample was monodisperse / Number of components: 5
Oligomeric State: FimD usher dimer in complex with one copy each of FimH, FimF, FimG pilins and FimC chaperone
MassTheoretical: 260 kDa / Experimental: 260 kDa

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Component #1: cellular-component, FimD-tip complex

Cellular-componentName: FimD-tip complex / a.k.a: Pilus assembly usher / Oligomeric Details: Dimer / Details: This component forms a dimer in the complex / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 96 kDa / Experimental: 96 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli b strain tuner (novagen) / bacteria / image: Escherichia coli
Vector: Tuner/pAN2 and pNH237
Source (natural)Location in cell: Outer membrane
External referencesGene Ontology: GO: 0015473 / InterPro: InterPro: 000015

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.04 mg/ml
Buffer solution: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
pH: 8
Support filmglow-discharged lacey carbon grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 108 K / Humidity: 85 % / Method: 6 seconds blot
Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F / Date: Feb 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Astigmatism: correction at 250,000 mag / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 5000 nm
Specimen HolderHolder: Gatan 626 cryo holder / Model: GATAN LIQUID NITROGEN / Temperature: 103 K ( 100 - 105 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 12.7 microns / Bit depth: 14 / OD range: 1.3

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 100 / Number of projections: 11000 / Details: particles were manually selected / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Cross-common lines / Software: EMAN, SPIDER / CTF correction: Each films / Resolution: 23 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
Details: Protocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera
Input PDB model: 1QUN
Chain ID: 1QUN_A

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