[English] 日本語
Yorodumi
- PDB-6gv9: Structure of the type IV pilus from enterohemorrhagic Escherichia... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6gv9
TitleStructure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC)
ComponentsPrepilin peptidase-dependent protein D
KeywordsPROTEIN FIBRIL / TYPE IV PILI EHEC T4P CELL ADHESION hemorrhagic coli pilus (HCP)
Function / homologyProkaryotic N-terminal methylation site / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site. / Prepilin peptidase-dependent pilin
Function and homology information
Specimen sourceEscherichia 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 supportFrance , 1件
OrganizationGrant numberCountry
French National Research AgencyFrance
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
DateDeposition: Jun 20, 2018 / Release: May 15, 2019Array

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0070
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0070
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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
Polymers208,37314
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Protein/peptide
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

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
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

-
Processing

EM software
IDNameVersionCategory
4CTFFIND3CTF correction
7Situsmodel fitting
12SPIDER3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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.

+
About Yorodumi

-
News

-
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

External links: EMDB at PDBe / Contact to PDBj

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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

Read more