|Entry||Database: EMDB / ID: 5009|
|Title||A cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.|
|Keywords||cryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis|
|Source||Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Map data||3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate|
|Method||single particle reconstruction, at 23 Å resolution|
|Authors||Tang C / Thanassi D / Li H|
|Citation||Cell, 2008, 133, 640-652|
|Date||Deposition: Mar 14, 2008 / Header (metadata) release: Mar 21, 2008 / Map release: Apr 22, 2009 / Last update: Apr 22, 2009|
Downloads & links
|File||emd_5009.map.gz (map file in CCP4 format, 3457 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.54 Å|
CCP4 map header:
-Entire FimD-tip complex
|Entire||Name: 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
|Mass||Theoretical: 260 kDa / Experimental: 260 kDa|
-Component #1: cellular-component, FimD-tip complex
|Cellular-component||Name: 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|
|Mass||Theoretical: 96 kDa / Experimental: 96 kDa|
|Source||Species: 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 references||Gene Ontology: GO: 0015473 / InterPro: InterPro: 000015|
|Sample solution||Specimen conc.: 0.04 mg/ml|
Buffer solution: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
|Support film||glow-discharged lacey carbon grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 108 K / Humidity: 85 % / Method: 6 seconds blot|
Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2010F / Date: Feb 1, 2007|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal) / Astigmatism: correction at 250,000 mag / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 5000 nm|
|Specimen Holder||Holder: Gatan 626 cryo holder / Model: GATAN LIQUID NITROGEN / Temperature: 103 K ( 100 - 105 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 12.7 microns / Bit depth: 14 / OD range: 1.3|
|Processing||Method: single particle reconstruction / Number of class averages: 100 / Number of projections: 11000 / Details: particles were manually selected / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Cross-common lines / Software: EMAN, SPIDER / CTF correction: Each films / Resolution: 23 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: 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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