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- EMDB-1953: Structure of the CS1 pilus of enterotoxigenic Escherichia coli re... -

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Basic information

Entry
Database: EMDB / ID: EMD-1953
TitleStructure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism
Map dataCS1-Group 3
Sample
  • Sample: CS1 pilus
  • Organelle or cellular component: CooA
Keywordspili / bacterial pathogenesis / colonization / virulence factor / donor strand complementarity / image reconstruction / helical symmetry / adhesion
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsGalkin VE / Kolappan S / Ng D / Zong Z / Li J / Yu X / Egelman EH / Craig L
CitationJournal: J Bacteriol / Year: 2013
Title: The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism.
Authors: Vitold E Galkin / Subramaniapillai Kolappan / Dixon Ng / ZuSheng Zong / Juliana Li / Xiong Yu / Edward H Egelman / Lisa Craig /
Abstract: Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine ...Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine via a variety of different pili. The CS1 pilus is a prototype for a family of related pili, including the CFA/I pili, present on ETEC and other Gram-negative bacterial pathogens. These pili are assembled by an outer membrane usher protein that catalyzes subunit polymerization via donor strand complementation, in which the N terminus of each incoming pilin subunit fits into a hydrophobic groove in the terminal subunit, completing a β-sheet in the Ig fold. Here we determined a crystal structure of the CS1 major pilin subunit, CooA, to a 1.6-Å resolution. CooA is a globular protein with an Ig fold and is similar in structure to the CFA/I major pilin CfaB. We determined three distinct negative-stain electron microscopic reconstructions of the CS1 pilus and generated pseudoatomic-resolution pilus structures using the CooA crystal structure. CS1 pili adopt multiple structural states with differences in subunit orientations and packing. We propose that the structural perturbations are accommodated by flexibility in the N-terminal donor strand of CooA and by plasticity in interactions between exposed flexible loops on adjacent subunits. Our results suggest that CS1 and other pili of this class are extensible filaments that can be stretched in response to mechanical stress encountered during colonization.
History
DepositionAug 24, 2011-
Header (metadata) releaseOct 3, 2012-
Map releaseOct 3, 2012-
UpdateMay 4, 2016-
Current statusMay 4, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1953.png

Downloads & links

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Map

FileDownload / File: emd_1953.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCS1-Group 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.16 / Movie #1: 4.16
Minimum - Maximum-1801.663085939999974 - 2109.639648440000201
Average (Standard dev.)3.46954131 (±181.903656009999992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.164.164.16
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-1801.6632109.6403.470

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Supplemental data

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Sample components

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Entire : CS1 pilus

EntireName: CS1 pilus
Components
  • Sample: CS1 pilus
  • Organelle or cellular component: CooA

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Supramolecule #1000: CS1 pilus

SupramoleculeName: CS1 pilus / type: sample / ID: 1000 / Oligomeric state: Oligomer / Number unique components: 1

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Supramolecule #1: CooA

SupramoleculeName: CooA / type: organelle_or_cellular_component / ID: 1 / Name.synonym: CS1 pilin / Oligomeric state: oligomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli) / Strain: LMC10 / synonym: ETEC / Cell: Escherichia coli strain LMC10 / Organelle: Pili / Location in cell: Cell surface
Molecular weightExperimental: 15 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 10 mM EDTA
StainingType: NEGATIVE / Details: 2% uranyl acetate
GridDetails: glow discharged continuous carbon coated grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DetailsLow dose mode
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 4.16 µm / Number real images: 10 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 80 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 30000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsPilus segments were selected using the helixboxer program in SPIDER.
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 111.9 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IHRSR

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Atomic model buiding 1

Initial modelPDB ID:

3s0v
PDB Unreleased entry


Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. A single subunit was manually docked using CHIMERA and the filament was built by applying the symmetry parameters for the reconstruction.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model


PDB Unreleased entry

PDB-3s0v:
Structure of the CooA pilin subunit from enterotoxigenic Escherichia coli

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