[English] 日本語
Yorodumi
- EMDB-0497: Cryo-EM reconstruction of CFA/I pili -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0497
TitleCryo-EM reconstruction of CFA/I pili
Map dataem-volume_P1
Sample
  • Complex: Enterotoxigenic Escherichia coli (ETEC) CFA/I pili
    • Protein or peptide: CFA/I fimbrial subunit B
KeywordsEnterotoxigenic Escherichia coli (ETEC) / CFA/I pili / helical reconstruction / PROTEIN FIBRIL
Function / homologyFimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli ETEC H10407 (bacteria) / ESCHERICHIA COLI ETEC O78:H12 (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZheng W / Andersson M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: IUCrJ / Year: 2019
Title: Cryo-EM structure of the CFA/I pilus rod.
Authors: Weili Zheng / Magnus Andersson / Narges Mortezaei / Esther Bullitt / Edward Egelman /
Abstract: Enterotoxigenic (ETEC) are common agents of diarrhea for travelers and a major cause of mortality in children in developing countries. To attach to intestinal cells ETEC express colonization ...Enterotoxigenic (ETEC) are common agents of diarrhea for travelers and a major cause of mortality in children in developing countries. To attach to intestinal cells ETEC express colonization factors, among them CFA/I, which are the most prevalent factors and are the archetypical representative of class 5 pili. The helical quaternary structure of CFA/I can be unwound under tensile force and it has been shown that this mechanical property helps bacteria to withstand shear forces from fluid motion. We report in this work the CFA/I pilus structure at 4.3 Å resolution from electron cryomicroscopy (cryo-EM) data, and report details of the donor strand complementation. The CfaB pilins modeled into the cryo-EM map allow us to identify the buried surface area between subunits, and these regions are correlated to quaternary structural stability in class 5 and chaperone-usher pili. In addition, from the model built using the EM structure we also predicted that residue 13 (proline) of the N-terminal β-strand could have a major impact on the filament's structural stability. Therefore, we used optical tweezers to measure and compare the stability of the quaternary structure of wild type CFA/I and a point-mutated CFA/I with a propensity for unwinding. We found that pili with this mutated CFA/I require a lower force to unwind, supporting our hypothesis that Pro13 is important for structural stability. The high-resolution CFA/I pilus structure presented in this work and the analysis of structural stability will be useful for the development of novel antimicrobial drugs that target adhesion pili needed for initial attachment and sustained adhesion of ETEC.
History
DepositionJan 24, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseSep 11, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.367
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.367
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nrv
  • Surface level: 0.367
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nrv
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0497.png

Downloads & links

-
Map

FileDownload / File: emd_0497.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.367 / Movie #1: 0.367
Minimum - Maximum-0.28369403 - 0.80672854
Average (Standard dev.)0.03286557 (±0.10784097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 139.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z139.520139.520139.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.2840.8070.033

-
Supplemental data

-
Sample components

-
Entire : Enterotoxigenic Escherichia coli (ETEC) CFA/I pili

EntireName: Enterotoxigenic Escherichia coli (ETEC) CFA/I pili
Components
  • Complex: Enterotoxigenic Escherichia coli (ETEC) CFA/I pili
    • Protein or peptide: CFA/I fimbrial subunit B

-
Supramolecule #1: Enterotoxigenic Escherichia coli (ETEC) CFA/I pili

SupramoleculeName: Enterotoxigenic Escherichia coli (ETEC) CFA/I pili / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)

-
Macromolecule #1: CFA/I fimbrial subunit B

MacromoleculeName: CFA/I fimbrial subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: ESCHERICHIA COLI ETEC O78:H12 (E. coli) / Strain: E7473
Molecular weightTheoretical: 14.968839 KDa
SequenceString:
VEKNITVTAS VDPAIDLLQA DGNALPSAVK LAYSPASKTF ESYRVMTQVH TNDATKKVIV KLADTPQLTD VLNSTVQMPI SVSWGGQVL STTAKEFEAA ALGYSASGVN GVSSSQELVI SAAPKTAGTA PTAGNYSGVV SLVMTLG

UniProtKB: CFA/I fimbrial subunit B

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 117011 / Software - Name: EMAN2
Startup modelType of model: NONE / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 113.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 97295

-
Atomic model buiding 1

Initial modelPDB ID:

3f85


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6nrv:
Cryo-EM reconstruction of CFA/I pili

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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