[English] 日本語
Yorodumi
- EMDB-1100: Structural insights into the assembly of the type III secretion n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1100
TitleStructural insights into the assembly of the type III secretion needle complex.
Map datanone
Sample
  • Sample: Needle Complex of the Type III Secretion from Salmonella typhimurium
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG
  • Protein or peptide: PrgJ
  • Protein or peptide: PRGI
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Salmonella tyhpimurium
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsMarlovits TC / Kubori T / Sukhan A / Thomas DR / Galan JE / Unger VM
CitationJournal: Science / Year: 2004
Title: Structural insights into the assembly of the type III secretion needle complex.
Authors: Thomas C Marlovits / Tomoko Kubori / Anand Sukhan / Dennis R Thomas / Jorge E Galán / Vinzenz M Unger /
Abstract: Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, ...Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, the needle complex, and its assembly precursor, the bacterial envelope-anchored base. Both the base and the fully assembled needle complex adopted multiple oligomeric states in vivo, and needle assembly was accompanied by recruitment of the protein PrgJ as a structural component of the base. Moreover, conformational changes during needle assembly created scaffolds for anchoring both PrgJ and the needle substructure and may provide the basis for substrate-specificity switching during type III secretion.
History
DepositionSep 28, 2004-
Header (metadata) releaseOct 21, 2004-
Map releaseDec 21, 2004-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.050322561
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.050322561
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1100.gif

Downloads & links

-
Map

FileDownload / File: emd_1100.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnone
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 0.0227 / Movie #1: 0.0503226
Minimum - Maximum-0.198282 - 0.318236
Average (Standard dev.)0.000171837 (±0.022488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 560 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1980.3180.000

-
Supplemental data

-
Sample components

-
Entire : Needle Complex of the Type III Secretion from Salmonella typhimurium

EntireName: Needle Complex of the Type III Secretion from Salmonella typhimurium
Components
  • Sample: Needle Complex of the Type III Secretion from Salmonella typhimurium
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG
  • Protein or peptide: PrgJ
  • Protein or peptide: PRGI

-
Supramolecule #1000: Needle Complex of the Type III Secretion from Salmonella typhimurium

SupramoleculeName: Needle Complex of the Type III Secretion from Salmonella typhimurium
type: sample / ID: 1000
Details: theoretical molecular weight for the base (without the needle filament and the inner rod) is approximately 2.7MDa
Oligomeric state: 20 / Number unique components: 5

-
Macromolecule #1: PrgH

MacromoleculeName: PrgH / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

-
Macromolecule #2: PrgK

MacromoleculeName: PrgK / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Salmonella tyhpimurium
Molecular weightExperimental: 28 MDa

-
Macromolecule #3: InvG

MacromoleculeName: InvG / type: protein_or_peptide / ID: 3 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightExperimental: 60 MDa

-
Macromolecule #4: PrgJ

MacromoleculeName: PrgJ / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightExperimental: 10 MDa

-
Macromolecule #5: PRGI

MacromoleculeName: PRGI / type: protein_or_peptide / ID: 5 / Recombinant expression: No
Source (natural)Organism: Salmonella tyhpimurium
Molecular weightExperimental: 8 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8 / Details: 10mM Tris-HCl 500mM NaCl 0.2% LDAO
GridDetails: 400 mesh Cu/Rh grid
VitrificationCryogen name: ETHANE / Details: Vitrification carried out in the cold room / Method: Blot for 15 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: 220,000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 79 / Average electron dose: 10 e/Å2 / Od range: 0.8 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsThe particles were selected interactively at the computer terminal.
CTF correctionDetails: phase flipping, each particle
Final reconstructionApplied symmetry - Point group: C20 (20 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: SPIDER, IMAGIC, MRC / Details: supervised projection matching procedure / Number images used: 1391

+
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://pdbjlvh1.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