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Yorodumi- EMDB-5009: A cryo-EM map of the FimD-tip complex, a bacterial surface pilus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5009 | |||||||||
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Title | A cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel. | |||||||||
Map data | 3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate | |||||||||
Sample |
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Keywords | cryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 23.0 Å | |||||||||
Authors | Tang C / Thanassi D / Li H | |||||||||
Citation | Journal: Cell / Year: 2008 Title: Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Authors: Han Remaut / Chunyan Tang / Nadine S Henderson / Jerome S Pinkner / Tao Wang / Scott J Hultgren / David G Thanassi / Gabriel Waksman / Huilin Li / Abstract: Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the ...Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the structural basis for pilus fiber assembly and secretion performed by the outer membrane assembly platform--the usher--is revealed by the crystal structure of the translocation domain of the P pilus usher PapC and single particle cryo-electron microscopy imaging of the FimD usher bound to a translocating type 1 pilus assembly intermediate. These structures provide molecular snapshots of a twinned-pore translocation machinery in action. Unexpectedly, only one pore is used for secretion, while both usher protomers are used for chaperone-subunit complex recruitment. The translocating pore itself comprises 24 beta strands and is occluded by a folded plug domain, likely gated by a conformationally constrained beta-hairpin. These structures capture the secretion of a virulence factor across the outer membrane of gram-negative bacteria. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5009.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-5009-v30.xml emd-5009.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_5009_1.tif | 750.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5009 | HTTPS FTP |
-Validation report
Summary document | emd_5009_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_5009_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_5009_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5009 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5009.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : FimD-tip complex
Entire | Name: FimD-tip complex |
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Components |
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-Supramolecule #1000: FimD-tip complex
Supramolecule | Name: FimD-tip complex / type: sample / ID: 1000 / Details: The sample was monodisperse Oligomeric state: FimD usher dimer in complex with one copy each of FimH, FimF, FimG pilins and FimC chaperone Number unique components: 5 |
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Molecular weight | Experimental: 260 KDa / Theoretical: 260 KDa |
-Supramolecule #1: FimD-tip complex
Supramolecule | Name: FimD-tip complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Pilus assembly usher / Details: This component forms a dimer in the complex / Number of copies: 1 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Ref GO | 0: GO:0015473 |
Ref INTERPRO | 0: IPR000015 |
Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: Outer membrane |
Molecular weight | Experimental: 96 KDa / Theoretical: 96 KDa |
Recombinant expression | Organism: Escherichia coli B strain Tuner (Novagen) / Recombinant plasmid: Tuner/pAN2 and pNH237 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.04 mg/mL |
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Buffer | pH: 8 / Details: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM. |
Grid | Details: glow-discharged lacey carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 108 K / Instrument: OTHER Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature Method: 6 seconds blot |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 100 K / Max: 105 K / Average: 103 K |
Alignment procedure | Legacy - Astigmatism: correction at 250,000 mag / Legacy - Electron beam tilt params: -2 mrad |
Date | Feb 1, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 100 / Average electron dose: 10 e/Å2 / Od range: 1.3 / Bits/pixel: 14 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 cryo holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | particles were manually selected |
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CTF correction | Details: Each films |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 11000 |
Final two d classification | Number classes: 100 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation |