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- PDB-6gv9: Structure of the type IV pilus from enterohemorrhagic Escherichia... -

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Basic information

Database: PDB / ID: 6gv9
TitleStructure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC)
ComponentsPrepilin peptidase-dependent protein D
Function / homologyProkaryotic N-terminal methylation site / integral component of membrane / Prepilin peptidase-dependent pilin
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8 Å
AuthorsBardiaux, B. / Amorim, G.C. / Luna-Rico, A. / Zheng, W. / Guilvout, I. / Jollivet, C. / Nilges, M. / Egelman, E. / Francetic, O. / Izadi-Pruneyre, N.
Funding support France, 1items
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.
Validation Report
SummaryFull reportAbout validation report
DepositionJun 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Deposited unit
A: Prepilin peptidase-dependent protein D
B: Prepilin peptidase-dependent protein D
C: Prepilin peptidase-dependent protein D
D: Prepilin peptidase-dependent protein D
E: Prepilin peptidase-dependent protein D
F: Prepilin peptidase-dependent protein D
G: Prepilin peptidase-dependent protein D
H: Prepilin peptidase-dependent protein D
I: Prepilin peptidase-dependent protein D
J: Prepilin peptidase-dependent protein D
K: Prepilin peptidase-dependent protein D
L: Prepilin peptidase-dependent protein D
M: Prepilin peptidase-dependent protein D
N: Prepilin peptidase-dependent protein D

Theoretical massNumber of molelcules
Total (without water)208,37314

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Protein
Prepilin peptidase-dependent protein D

Mass: 14883.821 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs0112 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8X974

Experimental details


EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

ComponentName: EHEC type IV pili / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 K

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.4 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1


EM software
4CTFFIND3CTF correction
7Situsmodel fitting
12SPIDER3D reconstruction
13PHENIXmodel refinement
Helical symmertyAngular rotation/subunit: 96 ° / Axial rise/subunit: 11.2 Å / Axial symmetry: C1
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25669 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / 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.

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