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- EMDB-0070: Structure of the type IV pilus from enterohemorrhagic Escherichia... -

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Basic information

Entry
Database: EMDB / ID: EMD-0070
TitleStructure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC)
Map data
SampleEHEC type IV pili:
Prepilin peptidase-dependent protein D
Function / homologyProkaryotic N-terminal methylation site / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site. / Prepilin peptidase-dependent pilin
Function and homology information
SourceEscherichia coli O157:H7 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 8 Å
AuthorsZheng W / Egelman E / Bardiaux B / Luna-Rico A / Izadi-Pruneyre N / Francetic O
CitationJournal: Structure / Year: 2019
Title: Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus.
Authors: Benjamin Bardiaux / Gisele Cardoso de Amorim / Areli Luna Rico / Weili Zheng / Ingrid Guilvout / Camille Jollivet / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic /
Abstract: Bacterial type 4a pili are dynamic surface filaments that promote bacterial adherence, motility, and macromolecular transport. Their genes are highly conserved among enterobacteria and their ...Bacterial type 4a pili are dynamic surface filaments that promote bacterial adherence, motility, and macromolecular transport. Their genes are highly conserved among enterobacteria and their expression in enterohemorrhagic Escherichia coli (EHEC) promotes adhesion to intestinal epithelia and pro-inflammatory signaling. To define the molecular basis of EHEC pilus assembly, we determined the structure of the periplasmic domain of its major subunit PpdD (PpdDp), a prototype of an enterobacterial pilin subfamily containing two disulfide bonds. The structure of PpdDp, determined by NMR, was then docked into the density envelope of purified EHEC pili obtained by cryoelectron microscopy (cryo-EM). Cryo-EM reconstruction of EHEC pili at ∼8 Å resolution revealed extremely high pilus flexibility correlating with a large extended region of the pilin stem. Systematic mutagenesis combined with functional and interaction analyses identified charged residues essential for pilus assembly. Structural information on exposed regions and interfaces between EHEC pilins is relevant for vaccine and drug discovery.
Validation ReportPDB-ID: 6gv9

SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.282
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.282
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gv9
  • Surface level: 0.282
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6gv9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0070.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 209.28 Å
1.09 Å/pix.
x 192 pix.
= 209.28 Å
1.09 Å/pix.
x 192 pix.
= 209.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.282 / Movie #1: 0.282
Minimum - Maximum-0.18283634 - 0.584637
Average (Standard dev.)0.013271507 (±0.06553787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 209.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z209.280209.280209.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.1830.5850.013

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Supplemental data

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Sample components

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Entire EHEC type IV pili

EntireName: EHEC type IV pili / Number of components: 2

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Component #1: protein, EHEC type IV pili

ProteinName: EHEC type IV pili / Recombinant expression: No
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #2: protein, Prepilin peptidase-dependent protein D

ProteinName: Prepilin peptidase-dependent protein D / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 14.883821 kDa
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 11.2 Å / Delta phi: 96 %deg;
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 297 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER / Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Soluble domain structure and homology model of TM segment fitted as rigid-bodies. Linker region built ab initio. Real-space refinement after symmetrization.
Output model

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