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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
Sample
  • Complex: EHEC type IV pili
    • Protein or peptide: Prepilin peptidase-dependent protein D
Function / homology: / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / membrane / Prepilin peptidase-dependent pilin
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsZheng W / Egelman E / Bardiaux B / Luna-Rico A / Izadi-Pruneyre N / Francetic O
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research Agency France
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.
History
DepositionJun 20, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseMay 15, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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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
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6gv9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0070.png

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

Histogram

Histogram (log scale)
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
Components
  • Complex: EHEC type IV pili
    • Protein or peptide: Prepilin peptidase-dependent protein D

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Supramolecule #1: EHEC type IV pili

SupramoleculeName: EHEC type IV pili / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Prepilin peptidase-dependent protein D

MacromoleculeName: Prepilin peptidase-dependent protein D / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Molecular weightTheoretical: 14.883821 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
FTLIELMVVI GIIAILSAIG IPAYQNYLRK AALTDMLQTF VPYRTAVELC ALEHGGLDTC DGGSNGIPSP TTTRYVSAMS VAKGVVSLT GQESLNGLSV VMTPGWDNAN GVTGWARNCN IQSDSALQQA CEDVFRFDDA N

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 96 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 25669
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

DetailsSoluble domain structure and homology model of TM segment fitted as rigid-bodies. Linker region built ab initio. Real-space refinement after symmetrization.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6gv9:
Structure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC)

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