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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: EMD-5009
TitleA cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.
Map data3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Sample
  • Sample: FimD-tip complex
  • Organelle or cellular component: FimD-tip complex
Keywordscryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsTang C / Thanassi D / Li H
CitationJournal: 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
DepositionMar 14, 2008-
Header (metadata) releaseMar 21, 2008-
Map releaseApr 22, 2009-
UpdateApr 22, 2009-
Current statusApr 22, 2009Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5009_1.tif

Downloads & links

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Map

FileDownload / File: emd_5009.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 96 pix.
= 241.3 Å		2.54 Å/pix.
x 96 pix.
= 241.3 Å		2.54 Å/pix.
x 96 pix.
= 241.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.74 / Movie #1: 2.3353526
Minimum - Maximum-4.68613 - 8.0905
Average (Standard dev.)0.00000000658932 (±0.871601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 241.3 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: FimD-tip complex
  • Organelle or cellular component: FimD-tip complex

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Supramolecule #1000: FimD-tip complex

SupramoleculeName: 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
Molecular weightExperimental: 260 KDa / Theoretical: 260 KDa

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Supramolecule #1: FimD-tip complex

SupramoleculeName: 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
Ref GO0: GO:0015473
Ref INTERPRO0: IPR000015
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: Outer membrane
Molecular weightExperimental: 96 KDa / Theoretical: 96 KDa
Recombinant expressionOrganism: Escherichia coli B strain Tuner (Novagen) / Recombinant plasmid: Tuner/pAN2 and pNH237

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
GridDetails: glow-discharged lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 108 K / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature
Method: 6 seconds blot

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 100 K / Max: 105 K / Average: 103 K
Alignment procedureLegacy - Astigmatism: correction at 250,000 mag / Legacy - Electron beam tilt params: -2 mrad
DateFeb 1, 2007
Image recordingCategory: 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 beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder: Gatan 626 cryo holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailsparticles were manually selected
CTF correctionDetails: Each films
Final reconstructionAlgorithm: 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 classificationNumber classes: 100

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Atomic model buiding 1

Initial modelPDB ID:

1qun


Chain - Chain ID: A
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation

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