|Entry||Database: PDB / ID: 6gv9|
|Title||Structure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC)|
|Components||Prepilin peptidase-dependent protein D|
|Keywords||PROTEIN FIBRIL / TYPE IV PILI EHEC T4P CELL ADHESION hemorrhagic coli pilus (HCP)|
|Function / homology||Prokaryotic N-terminal methylation site / integral component of membrane / Prepilin peptidase-dependent pilin|
Function and homology information
|Biological species||Escherichia coli O157:H7 (bacteria)|
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8 Å|
|Authors||Bardiaux, 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 |
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
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
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
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction|
|Component||Name: EHEC type IV pili / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Escherichia coli O157:H7 (bacteria)|
|Source (recombinant)||Organism: Escherichia coli BL21(DE3) (bacteria)|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 divisions/in.|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Average 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|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: 96 ° / Axial rise/subunit: 11.2 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25669 / Symmetry type: HELICAL|
|Atomic model building||Protocol: 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.
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.:Changes in new EM Navigator and Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi