[English] 日本語
Yorodumi
- EMDB-5009: A cryo-EM map of the FimD-tip complex, a bacterial surface pilus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5009
TitleA cryo-EM map of the FimD-tip complex, a bacterial surface pilus assembly intermediate in complex with the outer membrane secretion channel.
Map data3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Sample
  • Sample: FimD-tip complex
  • Organelle or cellular component: FimD-tip complex
Keywordscryo-electron microscopy / bacterial pilus / bacterial outer membrane secretion channel / pilus biogenesis
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsTang C / Thanassi D / Li H
CitationJournal: Cell / Year: 2008
Title: Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
Authors: Han Remaut / Chunyan Tang / Nadine S Henderson / Jerome S Pinkner / Tao Wang / Scott J Hultgren / David G Thanassi / Gabriel Waksman / Huilin Li /
Abstract: Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the ...Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the structural basis for pilus fiber assembly and secretion performed by the outer membrane assembly platform--the usher--is revealed by the crystal structure of the translocation domain of the P pilus usher PapC and single particle cryo-electron microscopy imaging of the FimD usher bound to a translocating type 1 pilus assembly intermediate. These structures provide molecular snapshots of a twinned-pore translocation machinery in action. Unexpectedly, only one pore is used for secretion, while both usher protomers are used for chaperone-subunit complex recruitment. The translocating pore itself comprises 24 beta strands and is occluded by a folded plug domain, likely gated by a conformationally constrained beta-hairpin. These structures capture the secretion of a virulence factor across the outer membrane of gram-negative bacteria.
History
DepositionMar 14, 2008-
Header (metadata) releaseMar 21, 2008-
Map releaseApr 22, 2009-
UpdateApr 22, 2009-
Current statusApr 22, 2009Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.33535264
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.33535264
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5009_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5009.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D Cryo-EM map of FimD-tip complex, a bacterial outer membrane pilus assembly intermediate
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level1: 1.74 / Movie #1: 2.3353526
Minimum - Maximum-4.68613 - 8.0905
Average (Standard dev.)0.00000000658932 (±0.871601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 241.3 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z959595
origin x/y/z0.0000.0000.000
length x/y/z241.300241.300241.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-4.6868.0910.000

-
Supplemental data

-
Sample components

-
Entire : FimD-tip complex

EntireName: FimD-tip complex
Components
  • Sample: FimD-tip complex
  • Organelle or cellular component: FimD-tip complex

-
Supramolecule #1000: FimD-tip complex

SupramoleculeName: FimD-tip complex / type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: FimD usher dimer in complex with one copy each of FimH, FimF, FimG pilins and FimC chaperone
Number unique components: 5
Molecular weightExperimental: 260 KDa / Theoretical: 260 KDa

-
Supramolecule #1: FimD-tip complex

SupramoleculeName: FimD-tip complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Pilus assembly usher / Details: This component forms a dimer in the complex / Number of copies: 1 / Oligomeric state: Dimer / Recombinant expression: Yes
Ref GOdivclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ...
divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00154 73ampajax1 classpoptr giGO001547 3ispandiv
Ref INTERPROdivclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ...
divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kIPR000015 ampajax1cl asspoptrgi IPR000015i spandiv
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: Outer membrane
Molecular weightExperimental: 96 KDa / Theoretical: 96 KDa
Recombinant expressionOrganism: Escherichia coli B strain Tuner (Novagen) / Recombinant plasmid: Tuner/pAN2 and pNH237

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.04 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl (pH 8), 0.15 M NaCl, 0.05% DDM.
GridDetails: glow-discharged lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 108 K / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. 12 degree Celsius chamber temperature
Method: 6 seconds blot

-
Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 cryo holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 100 K / Max: 105 K / Average: 103 K
Alignment procedureLegacy - Astigmatism: correction at 250,000 mag / Legacy - Electron beam tilt params: -2 mrad
DateFeb 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 100 / Average electron dose: 10 e/Å2 / Od range: 1.3 / Bits/pixel: 14

-
Image processing

CTF correctionDetails: Each films
Final two d classificationNumber classes: 100
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 11000
Detailsparticles were manually selected

-
Atomic model buiding 1

Initial modelPDB ID:

1qun


Chain - Chain ID: A
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. manual docking followed by local correlation based real space fitting in chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation

+
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